[Bioc-devel] bsseqData

Peter Hickey peter.hickey at gmail.com
Wed May 2 20:27:30 CEST 2018


Successful pushed to both devel and release. Thanks, Nitesh!

On Wed., 2 May 2018, 1:35 pm Turaga, Nitesh, <Nitesh.Turaga at roswellpark.org>
wrote:

> Try one more time please.
>
> I made some changes after seeing your output.
>
> Best,
>
> Nitesh
>
> > On May 2, 2018, at 1:21 PM, Peter Hickey <peter.hickey at gmail.com> wrote:
> >
> > Hi Nitesh,
> >
> > I did a fresh clone, updated the package, and committed the changes,
> > but am still unable to push to the bioc git repo. Requested output
> > below.
> >
> > $ git clone git at git.bioconductor.org:packages/bsseqData
> > # Make updates and commit
> > $ git push origin master
> > Counting objects: 7, done.
> > Delta compression using up to 4 threads.
> > Compressing objects: 100% (7/7), done.
> > Writing objects: 100% (7/7), 67.52 MiB | 1.35 MiB/s, done.
> > Total 7 (delta 2), reused 0 (delta 0)
> > remote: Error: file larger than 5 Mb.
> > remote:
> > remote:     File name: 'data/BS.cancer.ex.fit.rda'
> > remote:     File size: 41.5 Mb
> > remote:
> > remote: Please see Biocondcutor guidelines
> > remote: https://bioconductor.org/developers/package-guidelines/
> > remote:
> > To git.bioconductor.org:packages/bsseqData
> > ! [remote rejected] master -> master (pre-receive hook declined)
> > error: failed to push some refs to 'git at git.bioconductor.org:
> packages/bsseqData'
> >
> > $ git remote -v
> > origin git at git.bioconductor.org:packages/bsseqData (fetch)
> > origin git at git.bioconductor.org:packages/bsseqData (push)
> >
> > $ tree .git/hooks/
> > .git/hooks/
> > ├── applypatch-msg.sample
> > ├── commit-msg.sample
> > ├── post-update.sample
> > ├── pre-applypatch.sample
> > ├── pre-commit.sample
> > ├── pre-push.sample
> > ├── pre-rebase.sample
> > ├── pre-receive.sample
> > ├── prepare-commit-msg.sample
> > └── update.sample
> >
> > $ git branch -a
> > * master
> >  remotes/origin/HEAD -> origin/master
> >  remotes/origin/RELEASE_2_13
> >  remotes/origin/RELEASE_2_14
> >  remotes/origin/RELEASE_3_0
> >  remotes/origin/RELEASE_3_1
> >  remotes/origin/RELEASE_3_2
> >  remotes/origin/RELEASE_3_3
> >  remotes/origin/RELEASE_3_4
> >  remotes/origin/RELEASE_3_5
> >  remotes/origin/RELEASE_3_6
> >  remotes/origin/RELEASE_3_7
> >  remotes/origin/master
> >
> > $ git log
> > commit 5eb4c1ebc03fb1d713e873a77570744b94dc7659
> > Author: Peter Hickey <peter.hickey at gmail.com>
> > Date:   Wed May 2 13:14:24 2018 -0400
> >
> >    Run updateObject() on serialized objects
> >
> > commit 153db702379b926743f26012a34c8076b37f91f9
> > Author: Nitesh Turaga <nitesh.turaga at gmail.com>
> > Date:   Mon Apr 30 10:34:47 2018 -0400
> >
> >    bump x.y.z versions to odd y after creation of RELEASE_3_7 branch
> >
> > commit e02c0503b1f75b5ec4caffd055645d3b060d2af9
> > Author: Nitesh Turaga <nitesh.turaga at 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.hickey at gmail.com>
> > Date:   Sun Apr 29 12:31:34 2018 -0400
> >
> >    Bump minimum version of bsseq
> >
> > # git log output continues
> >
> >
> > On Wed, 2 May 2018 at 11:36 Turaga, Nitesh
> > <Nitesh.Turaga at roswellpark.org> wrote:
> >>
> >> Hi Pete,
> >>
> >> Can you try once again please? And this time send me the following
> information if it doesn’t work.
> >>
> >>        git remote -v
> >>
> >> and
> >>
> >>        ls -r (or tree) .git/hooks/
> >>
> >> and
> >>
> >>        git branch -a
> >>
> >>
> >> Thanks,
> >>
> >> Nitesh
> >>
> >>
> >>> On Apr 29, 2018, at 11:22 PM, Peter Hickey <peter.hickey at gmail.com>
> wrote:
> >>>
> >>> Sure thing, we'll wait. Thanks, Val
> >>>
> >>> On Sun., 29 Apr. 2018, 9:01 pm Obenchain, Valerie, <
> Valerie.Obenchain at roswellpark.org> wrote:
> >>> Hi guys,
> >>>
> >>> I'm not sure if this got resolved. If it didn't, I'd recommend waiting
> until after the 3.7 branching tomorrow.
> >>>
> >>> Thanks.
> >>> Val
> >>>
> >>>
> >>>
> >>> On 04/29/2018 09:37 AM, Peter Hickey wrote:
> >>>> I'm still unable to push large files after a fresh clone. I *am* able
> to push smaller changes (I just tweaked the DESCRIPTION to test this). But
> I get the "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.Turaga at roswellpark.org> wrote:
> >>>> Can you try with a fresh clone of the repo?
> >>>>
> >>>> Best,
> >>>>
> >>>> Nitesh
> >>>>
> >>>>> On Apr 29, 2018, at 10:21 AM, Peter Hickey <peter.hickey at 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 <
> Nitesh.Turaga at roswellpark.org> wrote:
> >>>>> Hi Pete,
> >>>>>
> >>>>> This should be resolved now.
> >>>>>
> >>>>> Best,
> >>>>>
> >>>>> Nitesh
> >>>>>> On Apr 29, 2018, at 9:50 AM, Peter Hickey <peter.hickey at gmail.com>
> 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 or am I doing something else wrong? bsseqData predates
> the svn
> >>>>>> -> git transition.
> >>>>>>
> >>>>>> Thanks,
> >>>>>> Pete
> >>>>>>
> >>>>>> $ git push origin master
> >>>>>> Counting objects: 7, done.
> >>>>>> Delta compression using up to 4 threads.
> >>>>>> Compressing objects: 100% (7/7), done.
> >>>>>> Writing objects: 100% (7/7), 66.80 MiB | 693.00 KiB/s, done.
> >>>>>> Total 7 (delta 2), reused 0 (delta 0)
> >>>>>> remote: Error: file larger than 5 Mb.
> >>>>>> remote:
> >>>>>> remote:     File name: 'data/BS.cancer.ex.fit.rda'
> >>>>>> remote:     File size: 40.8 Mb
> >>>>>> remote:
> >>>>>> remote: Please see Biocondcutor guidelines
> >>>>>> remote: https://bioconductor.org/developers/package-guidelines/
> >>>>>> remote:
> >>>>>> To git.bioconductor.org:packages/bsseqData.git
> >>>>>> ! [remote rejected] master -> master (pre-receive hook declined)
> >>>>>> error: failed to push some refs to
> >>>>>> 'git at git.bioconductor.org:packages/bsseqData.git'
> >>>>>>
> >>>>>>
> >>>>>> On Sat, 28 Apr 2018 at 19:17 Obenchain, Valerie <
> >>>>>> Valerie.Obenchain at roswellpark.org> wrote:
> >>>>>>
> >>>>>>> I've just given you and Pete access. Please give it a try and let
> me know
> >>>>>>> if you have problems.
> >>>>>>>
> >>>>>>> Val
> >>>>>>>
> >>>>>>> On 04/28/2018 10:50 AM, Kasper Daniel Hansen wrote:
> >>>>>>>
> >>>>>>> Could Pete and I get write access to bsseqData?
> >>>>>>>
> >>>>>>> Best,
> >>>>>>> Kasper
> >>>>>>>
> >>>>>>>       [[alternative HTML version deleted]]
> >>>>>>>
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