[Bioc-devel] Bioconductor 3.8 branch created

2018-10-30 Thread Obenchain, Valerie
The 3.8 branch has been created and commits can resume to 
git.bioconductor.org. If all goes as planned over the next 24 hours 
we'll announce the release tomorrow.

You have access to 2 versions of your package in git: "release" and 
"devel". Release is for bug fixes and documentation improvements only 
and devel is where regular development should happen.

Release:
Bioconductor version 3.8
Git branch RELEASE_3_8
R version 3.5.*

Devel:
Bioconductor version 3.9
Git branch master
R version 3.6.*

To continue using your existing clone be sure to pull the version bump 
and branch creation changes from Bioconductor.

Instructions for syncing:

https://bioconductor.org/developers/how-to/git/pull-upstream-changes/
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

Instructions for working with the branches:

https://bioconductor.org/developers/how-to/git/

If you have questions, please reply to this thread or post to the 
bioc-devel list at .

Thanks.
The Bioconductor team


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[Bioc-devel] Bioconductor 3.8 branching today

2018-10-30 Thread Obenchain, Valerie
Bioc developers,

Today we'll be creating the Bioconductor 3.8 branch starting at 11am 
EST. All commits to git.bioconductor.org will be blocked for about 2.5 
hours. We'll post back when push access is restored and you can resume 
commits.

Thanks.
The Bioconductor team


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agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
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this message in error, please notify the sender immediately by e-mail and 
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Re: [Bioc-devel] Need update access agaisnt package 'banocc'

2018-10-30 Thread Shepherd, Lori
The last push we had on the git server location was Oct 17th.

commit 9aee5761aaa97a063882a85295747640ec405dfb
Author: George Weingart 
Date:   Wed Oct 17 21:00:43 2018 -0700

Updated the version number



We have not received any valid push after this date and this is Version: 1.5.2 
as per the DESCRIPTION.  The package does not have a WARNING it has an ERROR 
but only in windows

 http://bioconductor.org/checkResults/devel/bioc-LATEST/banocc/



Your package will still be included in the release and we encourage you to look 
into this ERROR when you get a chance as having the package ERROR on windows 
will make in unavailable on this platform and lose a lot of potential users.  
Let us know if you are having any troubles with the ERROR by starting a post at 
bioc-devel@r-project.org


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of George 
Weingart 
Sent: Tuesday, October 30, 2018 1:27:10 AM
To: Turaga, Nitesh
Cc: Bioc-devel; Huttenhower, Curtis
Subject: Re: [Bioc-devel] Need update access agaisnt package 'banocc'

Could I trouble you to look at banocc 1.5.2 that I pushed: it has a
warning-
Is that ok or can we leave it like that to be released?

On Fri, Oct 19, 2018 at 4:07 PM George Weingart 
wrote:

> Could I trouble you to look at banocc 1.5.2 that I pushed: it has a
> warning-
> Is that ok or can we leave it like that to be released?
>
> On Thu, Oct 18, 2018 at 7:21 AM Turaga, Nitesh <
> nitesh.tur...@roswellpark.org> wrote:
>
>> 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
>>
>>
>>
>> > On Oct 18, 2018, at 10:03 AM, George Weingart <
>> george.weing...@gmail.com> wrote:
>> >
>> > Hello,
>> >
>> > Seems I have been able to push successfully but I do not see the build
>> report - Did I do something wrong or am I alooking at the wrong place?
>> > See enclosed screen print
>> >
>> > Thanks for your help !
>> >
>> > Tanias-MacBook-Air:banocc georgeweingart$ git push origin master
>> > Counting objects: 8, done.
>> > Delta compression using up to 4 threads.
>> > Compressing objects: 100% (8/8), done.
>> > Writing objects: 100% (8/8), 1.02 KiB | 1.02 MiB/s, done.
>> > Total 8 (delta 6), reused 0 (delta 0)
>> > To git.bioconductor.org:packages/banocc
>> >756f013..9aee576  master -> master
>> >
>> >
>> > On Thu, Oct 18, 2018 at 5:16 AM Turaga, Nitesh <
>> nitesh.tur...@roswellpark.org> wrote:
>> > > 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 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
>> > >   � HTTPS (public) read only access: https://git.bioconductor.org
>> > >
>> > >
>> > > Please check http://bioconductor.org/developers/how-to/git/.
>> > >
>> > > Also, http://bioconductor.org/developers/how-to/git/faq/ (#13).
>> > >
>> > > Best,
>> > >
>> > > Nitesh
>> > >
>> > >
>> > >> On Oct 17, 2018, at 9:57 PM, George Weingart <
>> george.weing...@gmail.com> wrote:
>> > >>
>> > >> Hi,
>> > >>
>> > >> This is a follow up to Valerie�s response in regards to the
>> permission to
>> > >> update �banocc�
>> > >>
>> > >> I am still getting an error message when I am trying to push:
>> > >>
>> > >>
>> > >> Tanias-MacBook-Air:banocc georgeweingart$ git push origin master
>> > >>
>> > >> fatal: remote error: FATAL: W any packages/banocc nobody DENIED by
>> fallthru
>> > >>
>> > >> (or you mis-spelled the reponame)
>> > >>
>> > >>
>> > >> Am I doing something wrong or am I still not permitted to update the
>> > >> repository ?
>> > >>
>> > >> Thanks!
>> > >>
>> > >> George Weingart PhD
>> > >>
>> > >> Huttenhower Lab
>> > >>
>> > >> Harvard School of Public Health
>> > >>
>> > >>
>> > >> DETAILS
>> > >>
>> > >> List of remotes
>> > >>
>> > >> Tanias-MacBook-Air:banocc georgeweingart$ git remote -v
>> > >>
>> > >> origin https://git.bioconductor.org/packages/banocc (fetch)
>> > >>
>> > >> origin https://git.bioconductor.org/packages/banocc (push)
>> > >>
>> > >> Log of the commits
>> > >>
>> > >> Tanias-MacBook-Air:banocc georgeweingart$ git log --oneline
>> > >>
>> > >> 9c411f9 (HEAD -> master) Modified DESCRIPTION to update contacts and
>> added
>> > >> parms to enable correct compile using C++11
>> > >>
>> > >>