[Bioc-devel] Git Transition Plan

Dear Bioconductor Developers, More news about the Git transition plan. We are coming close to our transition date and have made significant progress in getting our new server ready for the Bioconductor community. 1. Overall plan: - Bioconductor hosts each package as a distinct repository at

[Bioc-devel] Bioconductor's GIT transition

Dear Bioconductor Developers, Big news! We are planning to migrate from SVN to git. This is a major change in our version control model. We understand this may be disruptive to some developers and are working to make the transition as smooth as possible. The end goal is to provide a

Re: [Bioc-devel] git transition for projects with prior git history

I would be careful before using the --allow-unrelated-histories flag. Please investigate where there is a difference. Also, i don't understand why you are using the bioconductor-git-mirror? Your non-zero commit history should be related to bioconductor git server. Best Nitesh Get Outlook for

Re: [Bioc-devel] Git transition is happening August 16th.

Hi Maintainers, We are on schedule. The experiment-data package SVN commits have been disabled. The git transition for these packages is underway now with the latest snapshot. Best, Nitesh > On Aug 7, 2017, at 4:43 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> > wrote

Re: [Bioc-devel] Git transition is happening August 16th.

, Nitesh >> August 16th - 9am EST >> >> - Software package SVN commits are stopped, >> - About 6 hours after, the GIT server comes to life. >> - No SVN commits here after > On Aug 15, 2017, at 11:52 AM, Turaga, Nitesh <nitesh.tur...@roswellpar

Re: [Bioc-devel] unable to push local changes to bioconductor svn repository

cka <gosia.nowi...@uzh.ch> wrote: > > Hi, > > All is clear now. I will wait for the transition then. > > Thank you for all the help. > > Gosia > > >> On 10 Aug 2017, at 18:52, Turaga, Nitesh <nitesh.tur...@roswellpark.org> >> wrote: >>

Re: [Bioc-devel] git transition for projects with prior git history

erstanding of recommended practice. > If I try to merge bioconductor onto master, or vice versa, I get the > unrelated histories warning. Vlad's suggestion works, but results in > replaying ~700 commits onto the bioconductor repo...not so nice maybe. > > The https://github.com

Re: [Bioc-devel] git transition for projects with prior git history

ttps://github.com/Bioconductor-mirror/MAST.git repo is to make SVN > commits from the git tree. > > >> On Jul 28, 2017, at 11:33 AM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> >> wrote: >> >> I would be careful before using the --allow-unrelated-histories fla

Re: [Bioc-devel] unable to push local changes to bioconductor svn repository

In the meantime, You can choose to simply checkout the SVN repo, and commit directly to it. Nitesh > On Aug 10, 2017, at 12:46 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> > wrote: > > Hi Gosia, > > The cytofWorkflow was added to the wrong svn location, and t

Re: [Bioc-devel] git transition for projects with prior git history

The SVN repo is the most current version of your package as far as Bioconductor goes. Unfortunately, you have totally unrelated histories by the looks of it. (This should show up as an error, when you try to “merge”, i.e `git merge upstream/master`) I would suggest moving forward with the new

Re: [Bioc-devel] unable to push local changes to bioconductor svn repository

gosianow/cytofWorkflow.git (fetch) > originhttps://github.com/gosianow/cytofWorkflow.git (push) > > $ git branch -a > * master > remotes/origin/HEAD -> origin/master > remotes/origin/master > > > >> On 9 Aug 2017, at 16:37, Turaga, Nitesh <nitesh.tu

Re: [Bioc-devel] git transition for projects with prior git history

the old one for > reference. > > Thanks for the reply. > Kevin > > > On Thu, Aug 10, 2017 at 5:34 PM, Turaga, Nitesh > <nitesh.tur...@roswellpark.org> wrote: > Hi Kevin, > > If your Github and SVN repos separated so much, then I’d just wait for the &g

Re: [Bioc-devel] [Bioconductor/Contributions] DMCHMM (#430)

Hi Farhad, Please be patient. We are going to review your package soon. Best, Nitesh > On Aug 11, 2017, at 11:40 AM, Farhad Shokoohi wrote: > > Hello, > > Can you update me on the status of reviewing my package DMCHMM? > > Thank you > -- > Farhad Shokoohi, >

Re: [Bioc-devel] git transition for projects with prior git history

The SVN repo is the most current version of your package as far as Bioconductor goes. Unfortunately, you have totally unrelated histories by the looks of it. I would suggest moving forward with the new git repo, after the transition is done on August 16th. I would not “delete” the repository

Re: [Bioc-devel] Bioconductor git server beta testing begins now.

Dear Maintainers, For those of you who have submitted your public github id instead of your public SSH key, please make sure that the link `www.github.com/.keys` is valid and shows your SSH key. If that is not valid, we are not able to add your SSH key to the bioconductor server. Thanks,

[Bioc-devel] Maintainers submit your SSH public keys

Hi Maintainers, Please submit your (SSH public key or GitHub id) and SVN id in this google form https://goo.gl/forms/eg36vcBkIUjfZfLe2. It will only take a minute or less. This is a crucial step to the transition, which is going to happen soon. You will be able to test/complain/learn about the

Re: [Bioc-devel] Maintainers submit your SSH public keys

submit >a few days ago. Is there a way for me to confirm it has worked? > > >Best, > > >R. > > > >On Wed, 12-07-2017, at 14:50:14, Turaga, Nitesh ><nitesh.tur...@roswellpark.org> wrote: >> Hi Maintainers, >> >> Please submit your (SSH pub

Re: [Bioc-devel] Maintainers submit your SSH public keys

on the documentation, and FAQ section (https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/faq.md) Best Regards, Nitesh From: Samuel E Zimmerman <sezim...@einstein.yu.edu> Sent: Wednesday, July 12, 2017 11:49 AM To: Turaga, Nitesh; Ramon Diaz-Uriarte

Re: [Bioc-devel] Maintainers submit your SSH public keys

lto:jason.serv...@ki.se>> wrote: Hello, What exactly is ment with “Github id”? My Github username? Kind Regards, Jason On 12 Jul 2017, at 18:16, Turaga, Nitesh <nitesh.tur...@roswellpark.org<mailto:nitesh.tur...@roswellpark.org><mailto:nitesh.tur...@roswellpark.org<mailto

Re: [Bioc-devel] Bioconductor git server beta testing begins now.

clone https://git.bioconductor.org/packages/limma >svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/limma >--username readonly > >On Fri, Jul 7, 2017 at 9:42 PM, Turaga, Nitesh ><nitesh.tur...@roswellpark.org> wrote: >> Dear Maintainers, >> >> For t

Re: [Bioc-devel] git clarifications

Hi Michael, The Github webhook is only for you to submit your latest push to the build system during the package submission process. I don't think you will need this after, because once your package gets accepted there will be a nightly package build. So whatever you commit will get built

[Bioc-devel] Git transition: Missing SSH public keys on github.com

Hi, As we are processing the SSH keys today, we have noticed that a few people were having trouble submitting their keys. Maintainers should keep in mind that, they need to have their SSH public keys on Github, before submitting your Github_ID. So before you submit on the form, please

Re: [Bioc-devel] Git transition: Missing SSH public keys on github.com

Nitesh From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Turaga, Nitesh <nitesh.tur...@roswellpark.org> Sent: Wednesday, July 12, 2017 2:51:31 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Git transition: Missing SSH public keys on github.com Hi, As

Re: [Bioc-devel] Git Transition Plan

like to participate Von: "Turaga, Nitesh" <nitesh.tur...@roswellpark.org<mailto:nitesh.tur...@roswellpark.org>> An: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> Gesendet: Donnerstag, 1. Juni 2017 14:19:59 Betreff: Re: [Bio

[Bioc-devel] Bioconductor git server beta testing begins now.

>Dear Maintainers > >As announced earlier this year, Bioconductor is moving version control >systems from SVN to Git. > >The plan > > >- Software, experiment data, and workflow packages will be maintained > as git repositories created to capture the full commit history of > each

Re: [Bioc-devel] unable to push local changes to bioconductor svn repository

Hi Gosia, I tried to reproduce your error. But I’m not sure there have been any changes on either your Github repo, or your SVN. Both repositories are at the exact same location right now. Please try these commands on a “fresh” clone of your GitHub repo. $ git clone

[Bioc-devel] Git transition is happening August 16th.

Hello Maintainers, The details and timeline of the transition from SVN to GIT have been finalized. 1. Important Dates, Days of transition - August 15th and August 16th. August 15th - 9am EST - Git BETA server commits stop, BETA phase ends. All commits to the BETA repository are

Re: [Bioc-devel] unable to push local changes to bioconductor svn repository

ithub.com/gosianow/cytofWorkflow.git > remote.origin.fetch=+refs/heads/*:refs/remotes/origin/* > branch.master.remote=origin > branch.master.merge=refs/heads/master > svn-remote.devel.url=https://hedgehog.fhcrc.org/bioconductor//trunk/madman/Rpacks/cytofWorkflow > svn-remote.devel.fetch=:ref

Re: [Bioc-devel] Generate valid SSH keys for the bioc-git server!

ture Faculty Fellow > College of Computer and Information Science > Northeastern University > kuwisdelu.github.io<https://kuwisdelu.github.io> > > > > > On Aug 17, 2017, at 10:07 AM, Turaga, Nitesh > <nitesh.tur...@roswellpark.org<mailto:nitesh.tur...@ro

[Bioc-devel] Git merge conflict tags in certain packages. Please remove.

Hi Maintainers of the following packages, bioCancer Cardinal deltaGseg discordant DMRcate erccdashboard EventPointer ggtree gtrellis metagenomeFeatures OmicsMarkeR polyester ReportingTools rpx You have git merge conflict tags committed to your repository. Please makes sure these

Re: [Bioc-devel] Git transition is happening August 16th.

available through SVN remember to submit your SSH keys to https://goo.gl/forms/eg36vcBkIUjfZfLe2. NOTE: Workflow packages will remain on SVN for the moment. Best, Nitesh > On Aug 7, 2017, at 4:43 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> > wrote: > >

[Bioc-devel] SVN date stamping on vignette's does not work anymore.

Hi Maintainers, You have been using SVN properties to stamp dates in your vignettes. Since the git transition, this does not work anymore. These packages have been identified in this GitHub issue (https://github.com/Bioconductor/bioc_git_transition/issues/32). Best, Nitesh This email

[Bioc-devel] Generate valid SSH keys for the bioc-git server!

se issues. Thanks, Best, Nitesh > On Aug 16, 2017, at 9:05 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> > wrote: > > You have a malformed key. Please check the key you submitted. > > If you do not know what an SSH key is, > > https://www.bioconductor

Re: [Bioc-devel] Git Transition Plan

meone.org> >>> ``` >>> and then Bioc can use this mapping when exporting to Git? >>> >>> Finally, will people like me who already done the SVN-to-Git migration >>> be able to use that instead of the Bioc generated one? (I assume not, >>>

Re: [Bioc-devel] Unable to create a remote branch

It is trying to push to git.bioconductor.org. You probably don’t have your remotes set up right. Try `git remote -v` and paste the result. > On Sep 15, 2017, at 4:23 AM, Samuel Wieczorek wrote: > > Hi all, > > I try to create a remote branch but it fails. The

Re: [Bioc-devel] SSH keys

Hi, That is an invalid key. Please regenerate your key with the instructions provided in the http://bioconductor.org/developers/how-to/git/faq/ (FAQ section). Resubmit to the google-form. Best, Nitesh > On Sep 14, 2017, at 8:12 AM, Vojtech Kulvait wrote: > > Hi, > I

[Bioc-devel] Fwd: Getting w+r access for my package (IntEREst); svn/git transfer problem (Problem remains unsloved)

00014 University of Helsinki Finland. Email: ali.oghab...@helsinki.fi<https://webmail.helsinki.fi/horde/imp/dynamic.php?page=mailbox#> Phone: +358 50 4484569 ____ From: Turaga, Nitesh <nitesh.tur...@roswellpark.org<mailto:nitesh.tur...@roswellpark.org>>

Re: [Bioc-devel] Bioconductor failing package MEAL

used c.ruiz-arenas for MEAL and MultiDataSet. Finally, for the next > release, I got scoreInvHap accepted and I have now realized that I have > another svn user. What can I do to solve it? > > Thank you, > > Carlos Ruiz > > > > > El jueves, 14 de septiembre de

Re: [Bioc-devel] Bioconductor failing package MEAL

Hi Carlos, Do you by any chance have 2 separate SVN id’s? 1. c.ruiz 2. c.ruiz-arenas Best, Nitesh > On Sep 14, 2017, at 12:17 PM, Carlos Ruiz wrote: > > Hi, > Today I definitely was able to fetch from the Bioc git. However, I cannot > push. Here, the commands

Re: [Bioc-devel] Bioconductor failing package MEAL

uiz-arenas for MEAL and MultiDataSet. Finally, for the next > release, I got scoreInvHap accepted and I have now realized that I have > another svn user. What can I do to solve it? > > Thank you, > > Carlos Ruiz > > > > > El jueves, 14 de septiembre de 2017, Tu

Re: [Bioc-devel] Bioconductor failing package MEAL

hen, I used c.ruiz-arenas for MEAL and MultiDataSet. Finally, for the next >> release, I got scoreInvHap accepted and I have now realized that I have >> another svn user. What can I do to solve it? >> >> Thank you, >> >> Carlos Ruiz >> >> >> >&

Re: [Bioc-devel] hook declined error

Hi Anand, Each file needs to be smaller than 5Mb. If you have a file larger than 5mb, the pre-receive hook will tell you which file failed. Can you tell me why you are using “—force” or “-f” flag? We don’t allow force pushes to the bioconductor git server. Did you submit your SSH key to the

Re: [Bioc-devel] hook declined to update error

Hi Anand, Each file needs to be smaller than 5Mb. If you have a file larger than 5mb, the pre-receive hook will tell you which file failed. Can you tell me why you are using “—force” or “-f” flag? We don’t allow force pushes to the bioconductor git server. Try without it

Re: [Bioc-devel] maintain immunoClust

Hi, We have 2 keys on file for your package immunoClust, one is an ssh-dds key and the other is an ssh-rsa key, starting with: ssh-dss B3NzaC1kc3MAAACBAONrxcV+Ri07bvwAPLpPmzi8YvTiRQlgvT8P3P/wnFMwBUP4vmA9V2FTGSnYGJEURTznBrVvPgCy6 ssh-rsa

Re: [Bioc-devel] Bad keys

rm. Since then, I have tried to fetch upstream and continue to > get "host key verification failed." > > Again, my apologies for my confusion - any help you can provide would be much > appreciated. > > Sincerely, > > > > -Original Message- >

Re: [Bioc-devel] Errors updating DaMiRseq package

http://bioconductor.org/developers/how-to/git/sync-existing-repositories/ This should help you with the issue you are having. Please follow those steps. Best, Nitesh > On Sep 22, 2017, at 11:02 AM, Mattia Chiesa wrote: > > Dear all, > I am the mantainer of the

Re: [Bioc-devel] Unable to push to https://git.bioconductor.org/packages/GenomicTuples

I think my outlook messed up the formatting on my previous email, apologies. The origin is supposed to be g...@git.bioconductor.org:packages/GenomicTuples. You are currently using HTTP and are not able to push as a result of that. You can change your remote, git remote set-url origin

Re: [Bioc-devel] Unable to push to https://git.bioconductor.org/packages/GenomicTuples

Hi Peter, If you notice, On Sep 21, 2017, at 1:53 PM, Peter Hickey > wrote: Hi Nitesh, I'm unable to push changes to the GenomicTuples package to the BioC git host. $ git push fatal: remote error: FATAL: W any packages/GenomicTuples

Re: [Bioc-devel] Duplicate commit error on and off

Hi Thomas, The following issue occurred because there was a commit on Aug 17th with all the duplicates. Unfortunately, your upstream repository has been contaminated with duplicate commits. Till I figure out a solution on how to fix this, please hold off any further commits. I’ll keep you

Re: [Bioc-devel] Duplicate commit error on and off

Where is your primary development repo on Github? Please send me link. Best, Nitesh > On Oct 4, 2017, at 10:14 AM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> > wrote: > > Hi Thomas, > > The following issue occurred because there was a commit on Aug 17th wi

[Bioc-devel] Fwd: git svn permissions

Begin forwarded message: From: Thomas Lawson <thomas.nigel.law...@gmail.com<mailto:thomas.nigel.law...@gmail.com>> Subject: Re: [Bioc-devel] git svn permissions Date: October 3, 2017 at 12:37:14 PM EDT To: "Turaga, Nitesh" <nitesh.tur...@roswellpark.org<mailto:n

Re: [Bioc-devel] cherry picking fixes to release

site needs to be tweaked. > > Michael > > On Tue, Oct 3, 2017 at 11:15 AM, Turaga, Nitesh > <nitesh.tur...@roswellpark.org> wrote: >> I’m just guessing, but I think “git” is trying to work on the upstream >> RELEASE_3_5 directly. >> >> Maybe try, >&

Re: [Bioc-devel] EXTERNAL: Can't push to git

Hi I see that you have submitted your key multiple times. But missed one key component to get access to your package, i.e your previous SVN-ID given to your by bioconductor. You are supposed to submit your SVN ID in the google form, without with your keys will not get access. Best, Nitesh

Re: [Bioc-devel] EXTERNAL: Re: Enabling SSH keys

gs and errors I > need to fix. > Best regards > > On Tue, Oct 10, 2017 at 12:00 AM, Turaga, Nitesh > <nitesh.tur...@roswellpark.org> wrote: > You have to submit your SSH keys. > > Please read the bioconductor.org/developers/how-to/git/ > > Best, > > > &g

Re: [Bioc-devel] rcellminer Bioconductor package

You should have access if you have submitted the new key. We suggest your link your GitHub ID. And add keys to your Github, and we can get them from there. If you have submitted your GitHub ID once to the google form, you won’t have to resubmit. Best, Nitesh > On Oct 7, 2017, at 9:04 AM,

Re: [Bioc-devel] EXTERNAL: error: Could not fetch upstream

Hi We have a key on file for you. Your public key is ssh-rsa

Re: [Bioc-devel] EXTERNAL: error: Could not fetch upstream

OGhTLgaJlX9aaUNQ5RHOUIrr9pu/gkBD0c5C6FUe9GrlNrzr/fWtljEWEuD8ZevGX8mIEDU+Eh5Xk7ugN0soTdw== > ggl...@uwo.ca > > Greg > > >> On Oct 10, 2017, at 1:59 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> >> wrote: >> >> B3NzaC1yc2EDAQAB

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

Hi, What is the email you submitted with? So that I can check your submission. Nitesh > On Oct 10, 2017, at 3:57 PM, Van Twisk, Daniel > wrote: > > > > > > From: Vladislav Petyuk > Sent: Tuesday,

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

Please resubmit. > On Oct 10, 2017, at 4:24 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> > wrote: > > We do not have a submission with that email. > > Nitesh > >> On Oct 10, 2017, at 4:10 PM, Vladislav Petyuk <pet...@gmail.com> wrote: >&g

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

We do not have a submission with that email. Nitesh > On Oct 10, 2017, at 4:10 PM, Vladislav Petyuk <pet...@gmail.com> wrote: > > pet...@gmail.com > > On Tue, Oct 10, 2017 at 1:08 PM Turaga, Nitesh > <nitesh.tur...@roswellpark.org> wrote: > Hi, > > W

[Bioc-devel] Fwd: Duplicate commit error on and off

le but I think it has been disabled. Some of the Bioc/FAQs related to this topic indicate this too. Thomas On Wed, Oct 4, 2017 at 11:27 AM Turaga, Nitesh <nitesh.tur...@roswellpark.org<mailto:nitesh.tur...@roswellpark.org>> wrote: Thanks, I’ll get back to you. I wasn’t sure because the histo

Re: [Bioc-devel] Difficulty obtaining access to BioC git repository

pologize for my error and appreciate you > providing me with access. > > Thank you for your assistance with this. > > Best regards, > > Taylor > >> On Oct 5, 2017, at 12:04 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> >> wrote: >> &g

Re: [Bioc-devel] Duplicate commit error on and off

omas > > On Thu, Oct 5, 2017 at 9:36 AM Turaga, Nitesh <nitesh.tur...@roswellpark.org> > wrote: > It would be easier. I can do it and it would take you back to, > > commit c84c7b5fbdf1419af5030b66f8a759d29307f40b (git-svn) > Author: Herve Pages <hpa...@fhcrc.org>

Re: [Bioc-devel] Duplicate commit error on and off

c84c7b5f is the best option then let's do this. > > Just wondering, wouldn't it be much easier to run on your end > > git reset --hard <> > git merge --squash HEAD@{1} > > This would deduplicate everything without losing any commits. > > Thanks, > > Thomas &

Re: [Bioc-devel] Difficulty obtaining access to BioC git repository

Hi, You have submitted multiple times with bad ID’s. This has not gone too well with our application and fails add your key. You first submitted “rtraborn” with a set of keys, and then with the same set of keys with you valid SVN ID. The system does not add the same key twice with two separate

Re: [Bioc-devel] EXTERNAL: Permission Denied when pushing to bioc repo

submitted the package? > ________ > From: Turaga, Nitesh <nitesh.tur...@roswellpark.org> > Sent: Monday, October 16, 2017 2:23 PM > To: Thomas Sherman > Cc: bioc-devel@r-project.org > Subject: Re: EXTERNAL: [Bioc-devel] Permission Denied when pushing to bioc > repo

Re: [Bioc-devel] EXTERNAL: Permission Denied when pushing to bioc repo

Hi, Your SVN ID is t.sherman, you did not submit that in the google form. That is why you did not get access to your package, till now. For now, I’ve changed it to accept your current key. You should have access now. Please try again. Nitesh > On Oct 16, 2017, at 2:17 PM, Thomas Sherman

Re: [Bioc-devel] EXTERNAL: Git push error and duplicate commits

Hi Matthew, I remember fixing this repository for you a few weeks ago. You cannot push branches to the Bioconductor repository, that is in the FAQ, and documentation. Can you tell me what exactly are the steps you are trying that, you are getting duplicate commits again? Best, Nitesh >

Re: [Bioc-devel] EXTERNAL: Re: Difficulty obtaining access to BioC git repository

ent to me, and we were able > to sync from my Desktop computer; access from our two VMs failed, suggesting > that it’s an issue on that side of things. > > Thanks again for your help. I’ll let you know if we have any more questions. > > Best regards, > > Taylor > >

Re: [Bioc-devel] EXTERNAL: Unexpected message when using 'git commit'

Hi Your email and username, need to be the same as your Github ID. I’m not sure why you are trying to add "rabbitus@lumimacs-iMac.local” as your email and username. Could you please explain that? > On Oct 16, 2017, at 4:07 PM, cstrato wrote: > > Dear All, > > When I

Re: [Bioc-devel] EXTERNAL: Git push error and duplicate commits

ub.com/JinmiaoChenLab/cytofkit/commits/master_deprecated). Best, Nitesh > On Oct 13, 2017, at 2:18 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> > wrote: > > Hi Matthew, > > I’ll have to fix your branch again, for this I need some time. Do not push > any m

Re: [Bioc-devel] EXTERNAL: Permission denied for ImmuneSpaceR repo

Please send me a list of commands you have tried. I’d like to see the outputs as well. e.henrich has associated keys to it coming from www.github.com/immunespace.keys Best, Nitesh > On Oct 13, 2017, at 1:36 PM, Immune Space wrote: > > Hi Nitesh, > > We resubmitted

Re: [Bioc-devel] Cannot push to release branch

Hi Sam, Can you send me the exact command(s) you used to push changes to your RELEASE_3_5? Can you also show me the branch you are on when you push to RELEASE_3_5 (`git branch -a`), just copy/paste the output of that result. For more info, please check

Re: [Bioc-devel] failing Bioconductor package DeepBlueR

Hi Markus, Your SSH key has been accepted, but you don’t have access to the repository because the SVN system did not know you have access rights to this package. I’ll give you access rights to that package. Best Nitesh > On Sep 8, 2017, at 7:34 AM, Shepherd, Lori

Re: [Bioc-devel] Duplicate commit error on and off

dbTransaction(conn,dbGetQuery(conn, paste( > "INSERT INTO compound_descriptors(compound_id, > + dbTransaction(conn,dbExecute(conn, paste(" > INSERT INTO compound_descriptors(compound_id, >

Re: [Bioc-devel] Duplicate commit error on and off

. Thanks Nitesh (and your > colleagues) for doing all of this. It must have been a massive effort for so > many packages. > > Best, > > Thomas > > > On Fri, Sep 8, 2017 at 7:11 AM Martin Morgan <martin.mor...@roswellpark.org> > wrote: > On 09/08/2017 0

Re: [Bioc-devel] New pre-receive hook on git.bioconductor.org

lter. > > Stephanie > > On 8/30/17 5:15 AM, Turaga, Nitesh wrote: >> Hi Sean, >> A `git diff` between an "empty commit” (commit without a body, such >> as—`Creating branch for BioC 3.5 release`) and a commit with a body, >> results in an empty dif

Re: [Bioc-devel] Pushing changes to RELEASE_3_5

Hi Laurent, We are looking into it. Nitesh > On Aug 29, 2017, at 4:43 PM, Laurent Gatto wrote: > > > Dear Bioc devel, > > I am having issues pushing code to the latest release. I currently have > the following branches > > -> % git branch -a > * RELEASE_3_5 > master >

Re: [Bioc-devel] Pushing changes to RELEASE_3_5

e cases, the actual commit content > seems to be duplicated (for example re-generated Rd files). > > Hope this helps. > > Laurent > > On 29 August 2017 20:53, Turaga, Nitesh wrote: > >> Hi Laurent, >> >> We are looking into it. >>

Re: [Bioc-devel] Cannot push to master branch

You need to use the SSH protocol not HTTPS. So, your origin needs to be `g...@git.bioconductor.org:packages/MutationalPatterns.git`. http://bioconductor.org/developers/how-to/git/maintain-bioc-only/ > On Sep 11, 2017, at 10:26 AM, Janssen-10, R.R.E. > wrote: >

Re: [Bioc-devel] Upstream permission denied

Hi Your key will be added in the next run of our script. You can change your GitHub keys, our script will take in the new one, and you don’t have to resubmit on the google-form. It is run manually at the moment at noon EST everyday. Nitesh > On Sep 11, 2017, at 1:12 PM, Vladimir Kiselev

Re: [Bioc-devel] experimental data packages and git-lfs

Hi Levi, The external_data_store.txt file is not needed anymore. The current git.bioconductor.org server does not store files in the LFS mode, so you can just add a file, commit and push. But for Github, you might have to use LFS for such large files. I’ll look into this more and get back to

Re: [Bioc-devel] experimental data packages and git-lfs

gt; wrote: > > Thank you, Nitesh. Is there any difference at all now in how experimental > data vs. software packages are tracked and checked? > > On Tue, Sep 5, 2017 at 8:40 PM, Turaga, Nitesh > <nitesh.tur...@roswellpark.org> wrote: > Hi Levi, > > The external

Re: [Bioc-devel] problem with git / svn transition: ssh keys

Hi Luo, The key we have on file is missing the starting `ssh-rsa`. Could you please resubmit? Best, Nitesh > On Sep 7, 2017, at 5:04 PM, Luo Weijun wrote: > > Just want to make sure that you see my email below. I still have the same > problem at this time. > Weijun

Re: [Bioc-devel] Duplicate commit error on and off

Dear Thomas, Can you please send me the output of the two `git show` commands? > git show 8210e1e04e8dc6819b84820077293d8d61914cf5 > git show f514d35b793e1d9462b899bf3c76cc06ab4dcc91 I’ll need to take a look at those to advice accordingly. Best, Nitesh > On Sep 7, 2017, at 7:04 PM, Thomas

Re: [Bioc-devel] updating Bioconductor package that is already on Github

Hi Simina, Please try again now. The issue was you didn’t submit your SVN ID “s.boca”. This is needed for people who have been maintainers before the Git transition, to associate your key to the package. For new packages this issue doesn’t apply, because we just collect their Github IDs.

Re: [Bioc-devel] problem with git / svn transition: ssh keys

23 PM > > Nitesh, > I just submitted it. The problem is > gone indeed. > Could you process my request and assign > me the git access? Thanks. > Weijun > > > On Fri, 9/8/17, Turaga, Nitesh <nitesh.tur...@roswellpar

Re: [Bioc-devel] problem with git / svn transition: ssh keys

id_rsa": bad permissions > Permission denied (publickey). > fatal: Could not read from remote repository. > > Please make sure you have the correct access rights > and the repository exists. > > > On Tue, 9/12/17,

Re: [Bioc-devel] Bioconductor-mirror permanently removed August 25th

; > Jim > > On Thu, Aug 17, 2017 at 3:53 PM, Turaga, Nitesh > <nitesh.tur...@roswellpark.org> wrote: > Hi Maintainers, > > The https://github.com/Bioconductor-mirror is now stale after Bioconductor’s > git transition. We are no longer going to support it, and will be taki

[Bioc-devel] Fwd: Hook declined on a branch

Begin forwarded message: From: ni41435_ca > Subject: Re: [Bioc-devel] Hook declined on a branch Date: September 12, 2017 at 7:33:00 AM EDT To: Samuel Wieczorek > You

Re: [Bioc-devel] problem with git / svn transition: ssh keys

age too. > > > On Tue, 9/12/17, Turaga, Nitesh <nitesh.tur...@roswellpark.org> wrote: > > Subject: Re: problem with git / svn transition: ssh keys > To: "Luo Weijun" <luo_wei...@yahoo.com> > Cc: "Morgan, Ma

Re: [Bioc-devel] problem with git / svn transition: ssh keys

u have the correct access rights > and the repository exists. > > -------- > On Tue, 9/12/17, Turaga, Nitesh <nitesh.tur...@roswellpark.org> wrote: > > Subject: Re: problem with git / svn transition: ssh keys > To: "Luo Weijun" <luo_wei...@yahoo.com> > Cc: "Morgan, Ma

Re: [Bioc-devel] Need write permission for CNPBayes

Hi Rob, We have the a key on file for you and access to that package. Can you make sure you are using the same SSH key pair ? It starts with, ssh-rsa

Re: [Bioc-devel] SSH keys

Hi Vojtech, I have given you access to the blimaTestingData package. Please try to access it now with the same key you have for the blima package. Best, Nitesh > On Sep 25, 2017, at 7:18 AM, Vojtech Kulvait wrote: > > Hi, > I would like to ask you if I can push changes

Re: [Bioc-devel] Need write permission for CNPBayes

-T g...@git.bioconductor.org | grep 'CNPBayes' > R packages/CNPBayes > > Thanks- > > Rob > > > >> On Sep 25, 2017, at 5:32 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> >> wrote: >> >> >> Hi Rob, >> >> We

[Bioc-devel] Fwd: Failing package LEA

.ac.uk>> Subject: Re: Re: [Bioc-devel] Failing package LEA Date: September 29, 2017 at 8:46:31 AM EDT To: "Turaga, Nitesh" <nitesh.tur...@roswellpark.org<mailto:nitesh.tur...@roswellpark.org>> I am on annual leave until Friday 29 September 2017. Unless urgent, bear with

Re: [Bioc-devel] write access to RTNduals and RTNsurvival

; Mauro > > On 2 October 2017 at 10:50, Vinicius Saraiva Chagas > <chagas@gmail.com> wrote: >> Hello Nitesh, >> >> Thank you very much for the support. I totally agree with that. >> >> Best, >> Vinicius >> >> On Mon, Oct 2, 2017 at

Re: [Bioc-devel] write access to RTNduals and RTNsurvival

Hi Mauro Please always forward your git questions to bioc-devel. There is more than one person handling the issues about git. RTNsurvival, — Clari Groeneveld is the maintainer hence you don’t have write access. RTNduals — Vinicius Chagas is the listed maintainer on our system. This issue

Re: [Bioc-devel] git clone failed from git.bioconductor.org

You don’t seem to have an SSH public key on our system. Please submit your SSH public key. https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform If you have more questions, bioconductor.org/developers/how-to/git/faq/ Nitesh > On Oct 2, 2017, at

Re: [Bioc-devel] Several ssh keys ?

Hi, Good morning. You can do that. You have to add your new key to the google form. You can do that in two ways. 1. If you have submitted an SSH public key. (This is your case) — Submit a new ssh public key to the google form, but with the same SVN ID and email address. The google form

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