[Bioc-devel] bsseqData

Turaga, Nitesh Nitesh.Turaga at RoswellPark.org
Wed May 2 19:35:13 CEST 2018 

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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>>>>>>> 
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>>>>>> 
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>>>>>> 
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