Re: [Bioc-devel] Account acivation for Bioconductor Git repository

Hi, I have changed the email address associated with that account. Please login to the BiocCredentials app and add your SSH keys. You should be able to gain access to the Git repository then. https://git.bioconductor.org/BiocCredentials You’d first need to activate your account. Best,

Re: [Bioc-devel] github bridge to bioconductor

lopers tutorials, and 'git push' just kept telling me everything was up > to date. I started this package a few years ago when Bioc used SVN, and have > been confused ever since they moved to git and recommended I make a github > account. > Looking forward to seeing tonight's bui

Re: [Bioc-devel] github bridge to bioconductor

There is no bridge between GitHub and Bioconductor’s private git server. You have to push separately to the Bioconductor’s git server. Based on your setup, you have to do, git push upstream master which, pushes to g...@git.bioconductor.org:packages/rgsepd. Please let me know if you

Re: [Bioc-devel] Request to un-deprecate a package

Hi, “biocLite" will stay deprecated for R version 3.5.2. Please note that the issue is not with “biocLite" but with “mmnet". “mmnet” has been deprecated for R-3.5.z and is defunct for R-3.6.z. There are other workaround solutions to this, where you may install the package from the tarball

Re: [Bioc-devel] Pushing to upstream master

our git.bioconductor.org:packages/maftools repo synced with your GitHub now. Please check. Best, Nitesh > On Dec 18, 2018, at 11:12 AM, Turaga, Nitesh > wrote: > > Hi Anand, > > The issue is the way you have updated your version numbers. > > Note that the las

Re: [Bioc-devel] Additional developer

Hi Thomas, Your group member should have access to the repo now. Hi Daniela, Please check the email danicas...@gmail.com, for details on how to log in to BiocCredentials and activate your account. Best, Nitesh > On Dec 17, 2018, at 9:53 PM, Thomas Girke wrote: > > Dear Nitesh, > >

Re: [Bioc-devel] Pushing to upstream master

Hi Anand, The issue is the way you have updated your version numbers. Note that the last commit on upstream/master was the release version bump where your package has a version “1.9.0”. Please update the version to “1.9.1” and try pushing after the merge. I’ve outlined the steps you should

Re: [Bioc-devel] Pushing to upstream master

unterpart. Check out this branch and integrate the remote changes > hint: (e.g. 'git pull ...') before pushing again. > hint: See the 'Note about fast-forwards' in 'git push --help' for details. > > > >> On 17 Dec 2018, at 5:43 PM, Turaga, Nitesh >> wrote:

Re: [Bioc-devel] Giving Write Access

Hi Micheal, Please be informed that there can be only one “maintainer”. You may consider having more than one collaborator on the package, which is Benjamin Haibe Kains. Also, the email on file for Benjamin is "bhklab.resea...@gmail.com” with the username you have provided. I will add the

Re: [Bioc-devel] adding package maintainers

cial maintainer to my name? The > maintenance will be mainly implemented by me from now on. > > Best, > Jing > -Original Message- > From: Turaga, Nitesh [mailto:nitesh.tur...@roswellpark.org] > Sent: 13. joulukuuta 2018 16:46 > To: He, Liye ; Tang, Jing >

Re: [Bioc-devel] adding package maintainers

username is jtang920. > > Thanks a lot! > > Best, > Liye > From: Turaga, Nitesh > Sent: Wednesday, December 12, 2018 4:54:22 PM > To: He, Liye > Cc: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] adding package maintainers > > Please let us know who you wa

Re: [Bioc-devel] adding package maintainers

He, Liye wrote: > > Hi, > > Thanks for your reply. How about changing the maintainer? > > Best, > Liye > From: Turaga, Nitesh > Sent: Tuesday, December 4, 2018 6:55:23 PM > To: He, Liye > Cc: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] adding packa

Re: [Bioc-devel] email changed, can't access to my bioconductor package

Hi Yafeng, I have changed your email address in the app. You should be able to login with your new email address now. Please make sure to change the “maintainer” email address in the DESCRIPTION file of your package as well. Best, Nitesh > On Dec 4, 2018, at 9:19 PM, Yafeng Zhu wrote: >

Re: [Bioc-devel] adding package maintainers

Hi, Please cc the collaborator you’d like to add. We have to add the email to the BiocCredentials app before they get access to the Bioconductor git repo. But keep in mind, the person wouldn’t be a maintainer, but a contributor. Because R packages have only 1 official maintainer. It is

Re: [Bioc-devel] Cannot access remote upstream after changing the laptop

Hi, You should log in to the BiocCredentials app with the correct email registered on your package. You should then generate new keys on your laptop, and upload them on the BiocCredentials app. This will allow you to access your package again. http://bioconductor.org/developers/how-to/git/

Re: [Bioc-devel] bioconductor git credentials

ProtonMail Mobile > > > On Tue, Nov 20, 2018 at 22:03, Turaga, Nitesh > wrote: >> Hi Henning, >> >> Would you like the same email associated with the package as given in the >> DESCRIPTION file? If so, you should try to activate using the same email >>

Re: [Bioc-devel] bioconductor git credentials

Hi Henning, Would you like the same email associated with the package as given in the DESCRIPTION file? If so, you should try to activate using the same email address. (henning@gmail.com) Best Nitesh > On Nov 20, 2018, at 3:57 PM, Henning Redestig via Bioc-devel > wrote: > > Hi, >

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

Please try to activate your account now. I have updated your email address on our end. You will need to add SSH keys to your account once it is activated. Your ID is n.pavelka Best, Nitesh > On Nov 14, 2018, at 3:46 AM, Norman Pavelka wrote: > > normanpave...@gmail.com This email

Re: [Bioc-devel] Commits not appearing in bioconductor build

After a push is made it can take up to 48 hours for it to appear on the build report and landing pages - i.e. we do one pull, build, check, propagate in 24 hours - so if your commit was after the pull for the day it wont be until the following day.

Re: [Bioc-devel] Request upstream pull --force of sanitized master branch

n > one of the tests. > > thanks, > > - Sam > > > On 11/5/18 7:56 AM, Turaga, Nitesh wrote: >> External Email - Use Caution >> >> Hi Sam, >> >> I have updated your “master” branch on git.bioconductor.com to reflect what >> you

Re: [Bioc-devel] Request upstream pull --force of sanitized master branch

Hi Sam, I have updated your “master” branch on git.bioconductor.com to reflect what you have on GitHub, at https://github.com/rafalab/bumphunter. You will not get the duplicate commit error when you push to the master branch anymore. However, RELEASE_3_8 still has duplicate commits in the

Re: [Bioc-devel] query regarding bfg on bioconductor repository

in source and make files and shell scripts * checking for empty or unneeded directories * building 'restfulSE_1.4.0.tar.gz' Best, Nitesh > On Nov 2, 2018, at 12:54 PM, Turaga, Nitesh > wrote: > > Hello, > > Shweta, I have now fixed your package in “master” and “RELEASE_3_8

Re: [Bioc-devel] query regarding bfg on bioconductor repository

, rather than having to manually fix a repository. The main take away from this is that, it is extremely tedious to fix commit histories. If you have any questions about how I did this, I did the best I could to document the process and save original copies of the original repositories w

Re: [Bioc-devel] query regarding bfg on bioconductor repository

Hi Shweta, Please hold off making anymore commits to restfulSE. I’ve noticed some discrepancies in your package pre-release and post-release. I’ll try to correct it the best I can before letting you know. The issues seem to be two-fold, duplicate commits and unusually large file package.

Re: [Bioc-devel] Changing a name of a package already under review

It is be possible. While it’s in review, you can change the name of your package. I believe Lori, will have to do some magic to get the Single package builder to get the correct version. Best, Nitesh > On Oct 22, 2018, at 6:27 PM, Lan Huong Nguyen wrote: > > Hi, > > I was wondering if

Re: [Bioc-devel] Need update access agaisnt package 'banocc'

ackages/banocc >756f013..9aee576 master -> master > > > On Thu, Oct 18, 2018 at 5:16 AM Turaga, Nitesh > wrote: > > origin g...@git.bioconductor.org:packages/myPackage.git (fetch) > > origin g...@git.bioconductor.org:packages/myPackage.git (push) > >

Re: [Bioc-devel] Need update access agaisnt package 'banocc'

> origin g...@git.bioconductor.org:packages/myPackage.git (fetch) > origin g...@git.bioconductor.org:packages/myPackage.git (push) Typo in there, its “..org:packages/.." > On Oct 17, 2018, at 10:47 PM, Turaga, Nitesh > wrote: > > Your remotes should look li

Re: [Bioc-devel] Need update access agaisnt package 'banocc'

Your remotes should look like this, origin g...@git.bioconductor.org/packages/myPackage.git (fetch) origin g...@git.bioconductor.org/packages/myPackage.git (push) Access is through SSH protocol, not HTTPS. • SSH (developer) read / write access: g...@git.bioconductor.org •

Re: [Bioc-devel] Last build of Bioconductor 3.7

Hello Developers, Please note that the branch RELEASE_3_7 is now frozen. You cannot make any more changes as all the commits have been blocked. Best, Nitesh > On Oct 15, 2018, at 8:42 AM, Obenchain, Valerie > wrote: > > Developers, > > Tonight is the last build of Bioconductor 3.7.

Re: [Bioc-devel] Have trouble in push to master branch

er -> master (pre-receive hook declined) > error: failed to push some refs to > 'g...@git.bioconductor.org:packages/CRISPRseek.git' > > Best regards, > > Julie > > On 10/11/18, 1:43 PM, "Bioc-devel on behalf of Turaga, Nitesh" > > wrote: > &g

Re: [Bioc-devel] Have trouble in push to master branch

Hi Jianhong, I’m looking into it now. Nitesh > On Oct 11, 2018, at 1:35 PM, Jianhong Ou, Ph.D. wrote: > > Hi, > > I am trying to fix bug in my package. However, I got declined message: > > > git push upstream master > > Counting objects: 38, done. > > Delta compression using up to 8

[Bioc-devel] New Feature: Ability to control pre-receive hooks in a modular way is active

Hello Core team and Maintainers, We have just launched a new feature to regulate packages on git.bioconductor.org. The feature gives the core team, the ability to easily “disable" hooks for each package (software, data-experiment, and workflow) as needed. The hooks should be modified using

Re: [Bioc-devel] Why bioconductor?

As far as Levi’s comment about PEP8. It’s possible to design something similar with Jim Hester’s “lintr” package, which purely defines a style guide for code. https://github.com/jimhester/lintr > On Oct 10, 2018, at 3:16 PM, Levi Waldron wrote: > > A related comment came up in a conversation

Re: [Bioc-devel] Bad version number have been corrected for the following packages

Adding package “HiCDataHumanIMR90” to this list. Maintainer please be aware. > On Sep 27, 2018, at 12:50 PM, Turaga, Nitesh > wrote: > > Hi Maintainers, > > The packages mentioned below have malformed version number which is being > updated by me to 1.1.0 in t

[Bioc-devel] Bad version number have been corrected for the following packages

Hi Maintainers, The packages mentioned below have malformed version number which is being updated by me to 1.1.0 in this development cycle. This is because the ‘y' should usually be in the range 0-99, in the version format ‘x.y.z’. Please only update the ‘z’ when you make a change. During the

Re: [Bioc-devel] paxtoolsr Bioconductor Push Issues

Hi Augustin, Please remove the .Rproj file in your repository from git version control. You can add a .gitignore file, http://bioconductor.org/developers/package-guidelines/#gitignore Please check that link. Best, Nitesh > On Sep 24, 2018, at 12:15 PM, Turaga, Nitesh >

Re: [Bioc-devel] paxtoolsr Bioconductor Push Issues

ith the package. > > Augustin Luna > > On Mon, Sep 24, 2018 at 11:24 AM, Turaga, Nitesh > wrote: >> Hi Augustin, >> >> You should be able to push to your repository now. >> >> Please notify me once you have been able to push with the new .jar file, and >&

Re: [Bioc-devel] Create a new GitHub repository for an existing Bioconductor package

es > not have access to the email that he used to create his account on svn > (pme...@ulb.ac.be - given by his formal university) anymore since now he a > professor at another university. > > Ngoc > On 2018-09-24 16:32, Turaga, Nitesh wrote: >> Hi, >> >>

Re: [Bioc-devel] paxtoolsr Bioconductor Push Issues

Augustin Luna > > On Thu, Sep 20, 2018 at 4:50 PM, Turaga, Nitesh > wrote: >> Hi Augustin, >> >> There is a software package size limit to Bioconductor packages which is 5 >> MB. You cannot push because the pre-receive hook on the Bioconductor git >> repo is

Re: [Bioc-devel] Create a new GitHub repository for an existing Bioconductor package

nt now in order to do > so. > > Could you please give me some hints? > > Regards, > > Ngoc > > On 2018-09-24 13:09, Turaga, Nitesh wrote: >> Hi Ngoc, >> >> Please follow documentation we have put together on the Bioconductor website. >>

Re: [Bioc-devel] Create a new GitHub repository for an existing Bioconductor package

Hi Ngoc, Please follow documentation we have put together on the Bioconductor website. To help with your specific question http://bioconductor.org/developers/how-to/git/maintain-github-bioc/. For everything you’ll need after that, http://bioconductor.org/developers/how-to/git/ Best regards,

Re: [Bioc-devel] Git failing to push upstream to Bioc devel

t, working tree clean Now you should be able to push without the “force” option. Best, Nitesh > On Aug 31, 2018, at 8:32 PM, Koen Van den Berge > wrote: > > Hi, > > I did git pull, using `git pull upstream master`, first (see output); is this > insuf

Re: [Bioc-devel] Git failing to push upstream to Bioc devel

Hi, You cannot force push to git.bioconductor.org. Please "git pull" before you do anything else. Best Nitesh Get Outlook for Android From: Koen Van den Berge Sent: Friday, August 31, 8:01 PM Subject: [Bioc-devel] Git failing to push upstream to Bioc devel To:

Re: [Bioc-devel] GitHub and Bioc sync: issue with dup commit for the sva package

k declined to update refs/heads/master > To git.bioconductor.org:packages/sva.git > ! [remote rejected] master -> master (hook declined) > error: failed to push some refs to > 'g...@git.bioconductor.org:packages/sva.git' > > PS2 I did push the master_backup branch to

Re: [Bioc-devel] GitHub and Bioc sync: issue with dup commit for the sva package

Hi Leo, I’ll try to help you with this issue. The duplicates commit you have on your package “sva” come from the pre-git era of Bioconductor. There are three ways we can fix this, 1, You fix your GitHub repo by removing the duplicate commits. They happen only after this commit. commit

Re: [Bioc-devel] EXTERNAL: Updating SSH keys without previous email account

t; everywhere else apart from SSH key management. > > Many thanks > Anthony > > > On Fri, 3 Aug 2018, 19:10 Turaga, Nitesh, > wrote: > Hi Anthony, > > What is the new email you want associated with this package? > > Nitesh > > > On Aug 2, 2

Re: [Bioc-devel] EXTERNAL: troubles with fetching Bioconductor github

No, I'm not aware of any such issues. Maybe someone else in the community can chip in with some information about this. Best, Nitesh Get Outlook for Android<https://aka.ms/ghei36> From: Piotr Sent: Friday, August 3, 2018 5:22:23 AM To: Turaga, Nit

Re: [Bioc-devel] EXTERNAL: troubles with fetching Bioconductor github

@git.bioconductor.org:packages/BRAIN.git (push) > > bests, > Piotr > > On Thu, Aug 2, 2018 at 11:35 PM Turaga, Nitesh > wrote: > Please copy the result of this, > > git remote -v > > and send it to us so we have more information. > > http://bioconduc

Re: [Bioc-devel] EXTERNAL: troubles with fetching Bioconductor github

Please copy the result of this, git remote -v and send it to us so we have more information. http://bioconductor.org/developers/how-to/git/faq/ , check #14 Best, Nitesh > On Aug 2, 2018, at 5:14 PM, Piotr wrote: > > Dear All, > > I try to follow instruction here: >

Re: [Bioc-devel] EXTERNAL: permanent link to package

I think, http://bioconductor.org/packages/CAMTHC should be fine. This link is permanent, but the 10.18129/B9.bioc.CAMTHC link isn’t a bad idea as well. This DOI link just resolves to the original link ( http://bioconductor.org/packages/CAMTHC) anyway. Take a look a this too,

Re: [Bioc-devel] EXTERNAL: Re: Synching version numbers went wrong

Typo, I mean 1.7.1 > On Jul 30, 2018, at 10:38 AM, ni41435_ca > wrote: > > Hi Shana, > > It seems that this occurred because of a merge gone bad and then followed by > a series of version changes which are wrong. > > I’ll just fix your version number to (1.7.2) for now and it’s your >

Re: [Bioc-devel] EXTERNAL: Re: Synching version numbers went wrong

Hi Shana, It seems that this occurred because of a merge gone bad and then followed by a series of version changes which are wrong. I’ll just fix your version number to (1.7.2) for now and it’s your responsibility to sync again with your Github. Best, Nitesh > On Jul 30, 2018, at 5:51

[Bioc-devel] Fwd: Git error when pushing to bioconductor

b/scmeth The file that is causing the issue is called qcReport.Rmd. It is in the inst folder. Divy On Fri, Jun 22, 2018 at 12:57 PM, Turaga, Nitesh mailto:nitesh.tur...@roswellpark.org>> wrote: I don’t understand how that can happen. Are you following http://bioconductor.org

Re: [Bioc-devel] Including a submodule in the main package repository

Hi Tom, I agree with Kasper. It is far easier to maintain two repos and sync with your Bioconductor package as needed. We have no protocols in place or documentation in place to support submodules at the moment. I also want to add that your setup on GitHub is up to you as a maintainer and

Re: [Bioc-devel] Help with version numbering

Hi Rhonda, You can fix your version in your local repo. Just try to amend your commit if your version bump is in the most recent commit. You can try, "git commit --amend" This will allow you to fix your version number and try to push again. It hasn’t changed on the server side

Re: [Bioc-devel] mygene package - fixing build error

Hi Chunlei, You have to merge the changes into RELEASE_3_7 yourself and push. Please check the documentation on the website about how to push a fix to RELEASE_3_7 branch. http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ We create the branch automatically

Re: [Bioc-devel] undo decrease of package version

Hi Matthais, You can change your commit locally. Your version hasn’t been updated because the pre-receive hook has caught it. Just to further explain, “pre-receive” is before the the commit is received by the bioconductor server, so the version on the server is still correct and unchanged.

Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17

Hi Pijush You also might want to check the RSS feeds http://bioconductor.org/developers/gitlog/ to see if your package has been updated. Best, Nitesh > On Jun 14, 2018, at 3:43 AM, Pijush Das wrote: > > Dear Shepherd, Lori , > > > The DESCRIPTION file is already edited before in

Re: [Bioc-devel] Git error when pushing to bioconductor

to merge > the branches in some other way? > > Thank you, > Divy > > On Mon, Jun 4, 2018 at 8:10 AM, Turaga, Nitesh > wrote: > Hi Divy, > > It might be possible that you did not resolve all the conflicts you have. > > Generally, a `git status` will show you

Re: [Bioc-devel] Reverting to older version

ote: > > I was thinking to have an onAttach mentioning the issue and directing the > user to use the devel version to get around the issue...is that possible? > > - Original Message ----- > From: Turaga, Nitesh > To: Samsiddhi Bhattacharjee > Cc: Bioconductor Package

Re: [Bioc-devel] Git error when pushing to bioconductor

Hi Divy, It might be possible that you did not resolve all the conflicts you have. Generally, a `git status` will show you all the conflict files which are needed to be cleaned up by the merge. When you do a clean conflict resolution, you will be able to push cleanly to git.bioconductor.org.

Re: [Bioc-devel] MoonlightR maintainer

Hi Catharina, You should have access now. Best, Nitesh > On May 21, 2018, at 9:54 AM, Catharina Olsen wrote: > > Dear bioc-devel team, > > Antonio Colaprico and myself are listed as maintainers of MoonlighR. However, > I do not have access. Could you please add my

Re: [Bioc-devel] EXTERNAL: Re: Cannot update my development package to Bioconductor

Hi You have to fix the merge conflicts. Again, please take a look at the documentation on the website The canonical documentation for git: http://bioconductor.org/developers/how-to/git/ The documentation relevant to your problem:

Re: [Bioc-devel] EXTERNAL: Re: Cannot update my development package to Bioconductor

u do >> hint: not have locally. This is usually caused by another repository >> pushing >> hint: to the same ref. You may want to first integrate the remote changes >> hint: (e.g., 'git pull ...') before pushing again. >> hint: See the 'Note about fast-forwards' in 'git push -

Re: [Bioc-devel] Cannot update my development package to Bioconductor

Did you try to ‘git pull’ as mentioned in the error message? Best, Nitesh > On May 14, 2018, at 2:48 PM, cstrato wrote: > > Dear GIT experts, > > On Saturday I wanted to update my development package to xps_1.41.1, however > until now it was not updated in the 'Multiple

Re: [Bioc-devel] Using https to maintain a package

Hi, Sean is correct. There is only read-only access available through HTTP. You would need SSH access for read-write privileges at the moment. We show this in the package landing pages. As you scroll to “Package Archives”, you will notice 'Source repository’, and 'Source Repository (Developer

Re: [Bioc-devel] bsseqData

uthor: Nitesh Turaga <nitesh.tur...@gmail.com> > Date: Mon Apr 30 10:31:27 2018 -0400 > >bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch > > commit 3f87e4d027264396bdeeeb87baa68fb3b6662b46 > Author: Peter Hickey <peter.hic...@gmail.com&

Re: [Bioc-devel] bsseqData

"Error: file larger than 5 Mb" error when I try to update larger >> objects (e.g., BS.cancer.ex.fit.rda which is 40.8 Mb). >> >> On Sun, 29 Apr 2018 at 11:43 Turaga, Nitesh <nitesh.tur...@roswellpark.org> >> wrote: >> Can you try with a fresh clo

Re: [Bioc-devel] The following bioconductor packages have duplicate commits

an > GitHub: https://github.com/cafletezbrant/flowClean > > On Tue, May 1, 2018 at 9:59 AM, Turaga, Nitesh > <nitesh.tur...@roswellpark.org> wrote: > Hello Maintainers, > > Once you have resolved your package, please let me know both your package > name, and GitHub

Re: [Bioc-devel] The following bioconductor packages have duplicate commits

> Thanks Nitesh. > > Following the manual [1] I believe I have resolved this issue. > > [1] > https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github- > > On Mon, Apr 30, 2018 at 1:34 PM, Turaga, Nitesh > <nitesh.tur...@roswellpa

[Bioc-devel] The following bioconductor packages have duplicate commits

Hi Maintainers, We just concluded the bump in the RELEASE_3_7 branch and master. But, the following packages have a history of duplicate commits and we are leaving it up to the maintainers to fix these duplicate commits. There were 12 software packages that had duplicate commits. Please fix

Re: [Bioc-devel] Switch to SSH protocol for git clone instructions on package landing pages?

Hi Pete, For developers there is no reason not to use the SSH protocol. But there are many people who’d like to clone the repo and look at it on their local machine. Take for example packages which are not maintained on both the bioconductor server and Github. For these packages, a good way

Re: [Bioc-devel] bsseqData

Can you try with a fresh clone of the repo? Best, Nitesh > On Apr 29, 2018, at 10:21 AM, Peter Hickey <peter.hic...@gmail.com> wrote: > > Nitesh, I am still getting the "Error: file larger than 5 Mb" error. > > On Sun, 29 Apr 2018 at 09:59 Turaga, Nitesh

Re: [Bioc-devel] bsseqData

Hi Pete, This should be resolved now. Best, Nitesh > On Apr 29, 2018, at 9:50 AM, Peter Hickey wrote: > > Thanks, Val. I'm getting an error about "too large files" when I try to > push (see below). Is there a different workflow for pushing an experiment > data package

Re: [Bioc-devel] Process to rename a bioconductor package

Hi Adrian, I’ve changed your package name from roma to “OmaDB”. You should change your GitHub repo’s name as well "https://github.com/klarakaleb/roma” —> https://github.com/klarakaleb/OmaDB. You can do this by, https://github.com/klarakaleb/roma/settings, and there will be an option to

Re: [Bioc-devel] deleting irrelevant legacy objects from git repo?

Ok, please check if everything on the master branch is as expected. I’ve synced it. Best Nitesh > On Apr 24, 2018, at 11:20 AM, Alexander Pico <alex.p...@gladstone.ucsf.edu> > wrote: > > It’s ready. Thanks! > > - Alex > >> On Apr 24, 2018, at 8:

[Bioc-devel] Fwd: Failing package merhr

Begin forwarded message: From: 露崎 弘毅 <k.t.the-ans...@hotmail.co.jp<mailto:k.t.the-ans...@hotmail.co.jp>> Subject: RE: Failing package merhr Date: April 24, 2018 at 11:07:15 AM EDT To: "Turaga, Nitesh" <nitesh.tur...@roswellpark.org<mailto:nitesh.tur...@roswellpark.o

Re: [Bioc-devel] deleting irrelevant legacy objects from git repo?

t.bioconductor.org:packages/RCy3.git > > Thanks! > - Alex > >> On Mar 19, 2018, at 11:29 AM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> >> wrote: >> >> Another note, it is not be possible for you to push back to the Bioconductor >> server once the r

Re: [Bioc-devel] I could't push My package GMRP to github/master

Hi Yuande, Please try to follow the commands on the documentation line by line. http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ Follow these instructions as is, and please send me the output of each command. Best, Nitesh > On Apr 23, 2018, at 7:53 PM, Yuande Tan

Re: [Bioc-devel] Unable to push to origin master

ductor upstream. I > guess it’s not that important but in case others have the same problem it > would be nice to know. > > Giorgio > >> On Apr 23, 2018, at 19:18, Turaga, Nitesh <nitesh.tur...@roswellpark.org> >> wrote: >> >> Hi Giorgio, >> >

Re: [Bioc-devel] Unable to push to origin master

Hi Giorgio, This is an issue with Github. They have a pre-receive hook on Github’s end which is being triggered. Do you get the same error message when you push to Bioconductor (upstream)? (git push upstream master) I’m not sure why you are getting an error with that .rb (ruby) extension.

Re: [Bioc-devel] git push confusion

h other than "master"? How can I tell what the build servers are using ? > > On Mon, Apr 23, 2018 at 11:14 AM, Turaga, Nitesh > <nitesh.tur...@roswellpark.org> wrote: > Please check out the documentation > > http://bioconductor.org/developers/how-to/git/push-t

Re: [Bioc-devel] git push confusion

ioconductor.org:packages/rgsepd.git (push) > > > And when I do various push commands they say "everything up to date" > But I want to make sure the bioc servers get the update before the 3.7 > lockdown. Is there any way to see what the are holding ? > > >

Re: [Bioc-devel] git push confusion

Hi Karl, Bioconductor doesn’t automatically grab changes from your Github. A large body of the work is maintained only on our Bioconductor git server. The maintainer has to push to both Github and the Bioconductor server if the changes have to propagate. RELEASE_3_6 is now frozen forever. We

Re: [Bioc-devel] Transition from Google Sheet to Web App

The Web App for managing SSH keys is now available at https://git.bioconductor.org/BiocCredentials/ Accounts have been created for all package maintainers. Note the central identifier, i.e., how you login is your email. This email was taken from the DESCRIPTION of your package or the Google

Re: [Bioc-devel] Can not push to bioconductor! please help me!

Hi Zhu, You submitted your keys with the wrong username. Please use your SVN ID “m.zhu” and resubmit Best, Nitesh > On Apr 16, 2018, at 12:32 PM, Zhu MF wrote: > > dear sir: > > > contents in GitHub and that in bioconductor are not the same. I want to > update the

Re: [Bioc-devel] Bioconductor Git Access: GateFinder

ccess by using `ssh -T g...@git.bioconductor.org`. Best, Nitesh > On Apr 13, 2018, at 2:43 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> > wrote: > > Hi Tony, > > You don’t have access to that package. I’ve checked the package DESCRIPTION > and there is no recor

[Bioc-devel] Fwd: Bioconductor Git Access: GateFinder

lto:g...@git.bioconductor.org>:packages/GateFinder.git (push) ssh -T g...@git.bioconductor.org<mailto:g...@git.bioconductor.org> command lists all packages as read only On Fri, Apr 13, 2018 at 10:59 AM, Turaga, Nitesh <nitesh.tur...@roswellpark.org<mailto:nitesh.tur...@roswellpark.org>> wr

Re: [Bioc-devel] Bioconductor Git Access: GateFinder

@git.bioconductor.org:packages/GateFinder.git (push) > > ssh -T g...@git.bioconductor.org command lists all packages as read only > > On Fri, Apr 13, 2018 at 10:59 AM, Turaga, Nitesh > <nitesh.tur...@roswellpark.org> wrote: > You are using the HTTPS protocol instead of SSH.

Re: [Bioc-devel] Bioconductor Git Access: GateFinder

You are using the HTTPS protocol instead of SSH. Please refer to http://bioconductor.org/developers/how-to/git/faq/ (#13). Your upstream should look like “g...@git.bioconductor.org:packages/GateFinder.git”. Nitesh > On Apr 13, 2018, at 1:44 PM, Tony Culos wrote: > >

[Bioc-devel] RELEASE_3_6 branch frozen at 3:00pm EST today

Hello Maintainers, The commits to RELEASE_3_6 will be blocked at 3:00pm EST today. Best, Nitesh > On Apr 10, 2018, at 5:03 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> > wrote: > > Hello Maintainers, > > We are going to block pushes to the RELEASE_3_6 bran

Re: [Bioc-devel] Unable to access repository

t;>>> 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 notified that any disclosure, copying, >>>> distribution, or use of this

Re: [Bioc-devel] Unable to access repository

Hi, The only key available on that package is “j.saezrodriguez”, and there is no key available with that username. I’m not sure how you’ve had previous access to this package after we’ve moved the Git repository. Can you upload a key under the username: clarepacini, and please have Julio

[Bioc-devel] RELEASE_3_6 branch frozen at 3:00pm EST tomorrow

Hello Maintainers, We are going to block pushes to the RELEASE_3_6 branch tomorrow at 15:00 EST. Maintainers who were planning to commit have until tomorrow 15:00 EST (3pm EST) to fix any outstanding issues they have. NOTE: Once the builds are done, the Bioconductor RELEASE_3_6 branch will be

[Bioc-devel] Matrix::(cBind|rBind) to base::(cbind|rbind)

Hello Maintainers, The following packages have been identified for changing the functions ‘Matrix::cBind’ and ‘Matrix::rBind’ to the ‘base::cbind’ and ‘base::rbind’. The functions ‘Matrix::cBind’ and ‘Matrix::rBind’ have been deprecated by the author of the Matrix package.

Re: [Bioc-devel] Need some help to submit a R package.

Hi, Please read through this documentation. http://bioconductor.org/developers/package-submission/ Nitesh > On Apr 2, 2018, at 2:00 AM, Pijush Das wrote: > > Dear Sir, > > > > I have developed an R package. I want to submit this package in > Bioconductor. > Please

Re: [Bioc-devel] GUIDEseq problems reported in the Multiple platform build/check report for BioC 3.6

h, > > I will try it. Since it is a released version, I thought I will first get > your input . > > Thanks! > > Best regards, > > Julie > >> On Mar 29, 2018, at 1:59 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> >> wrote: >>

Re: [Bioc-devel] GUIDEseq problems reported in the Multiple platform build/check report for BioC 3.6

Hi Julie, Did you try #8 from the documentation pointed out by the error message? Take a look at the documentation to fix this, https://bioconductor.org/developers/how-to/git/sync-existing-repositories/, particularly, point #8 (force Bioconductor master to Github master). The idea is to force

Re: [Bioc-devel] Moving Package from SVN to Git

I just processed the keys today. Please try again. Best, Nitesh > On Mar 28, 2018, at 1:12 PM, Tomasz Stokowy wrote: > > Dear bioc-devel, > > I am moving my package RareVariantVis to GitHub following steps listed here: >

Re: [Bioc-devel] git push complains non-existing files being too big

to benefit. > > Best regards, > > Julie > > On 3/26/18, 3:39 PM, "Turaga, Nitesh" <nitesh.tur...@roswellpark.org> wrote: > >Hi Julie, > > > >Please send this email to the bioc-devel page. It’s a very valid question > and

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