[Bioc-devel] Package not updated in build system from github

[Panagiotis Moulos]

Thank you Martin! I had missed that part. Indeed maybe you can update the
instructions for non-git masters (like me).

On Fri, Aug 25, 2017 at 1:14 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

> On 08/25/2017 03:36 AM, Panagiotis Moulos wrote:
>
>> Dear all,
>>
>> For some time now, my package metaseqR fails to pass the checks at the
>> build system
>>
>> http://bioconductor.org/checkResults/3.6/bioc-LATEST/metaseqR/
>>
>> Although I am not sure I understand the source of the problem (all is well
>> in my local systems),
>>
>> "Error : object ‘vsn’ is not exported by 'namespace:vsn'"
>>
>> I tried a couple of fixes to see if the problem goes away. However, it
>> seems that the package is not updated in the build system, although I
>> bumped the "z" version from x.y.z (1.17.0 to 1.17.2) for some time now (
>> https://github.com/pmoulos/metaseqR).
>>
>> I suppose I have correctly followed the instructions here (
>> http://bioconductor.org/developers/how-to/git/maintain-github-bioc/)
>> since
>> I didn't receive any errors/warnings and all seem ok in the repository.
>>
>
> The scenario describes how to establish the git repo. Once established,
> you need to push changes to github
>
>   git push origin master
>
> (I guess you've already done that) and to bioconductor
>
>   git push upstream master
>
> following
>
>   http://bioconductor.org/developers/how-to/git/push-to-github-bioc/
>
> I'll update the instructions in this scenario to make this clear.
>
> One way of seeing recent commits is to make a temporary 'shallow' clone of
> the repository
>
> The are no changes in Bioconductor's git. You can quickly see the last
> commit by changing to a separate directory and
>
> /tmp$ git clone --depth 1 git at git.bioconductor.org:packages/metaseqR
> Cloning into 'metaseqR'...
> remote: Counting objects: 173, done.
> remote: Compressing objects: 100% (170/170), done.
> remote: Total 173 (delta 17), reused 0 (delta 0)
> Receiving objects: 100% (173/173), 1.41 MiB | 2.56 MiB/s, done.
> Resolving deltas: 100% (17/17), done.
> Checking connectivity... done.
> /tmp$ cd metaseqR/
> tmp/metaseqR$ git log --all
> commit c531533fe9ebb7918e79d4ef09d8c694737379b9
> Author: Herve Pages <hpages at fhcrc.org>
> Date:   Mon Apr 24 19:50:57 2017 +0000
>
>     bump x.y.z versions to odd y after creation of 3_5 branch
>
>     git-svn-id: file:///home/git/hedgehog.fhcr
> c.org/bioconductor/trunk/madman/Rpacks/metaseqR at 129129
> bc3139a8-67e5-0310-9ffc-ced21a209358
>
>
>
> Martin
>
>
>> Any suggestions are most welcome. Thanks in advance.
>>
>> Panagiotis
>>
>>
>
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-- 
*Panagiotis Moulos, PhD*
*Post doctoral researcher in Bioinformatics,*
*BSRC 'Alexander Fleming'*
*Fleming 34, 16672, Vari, Greece*
*Tel: +30 210 9656310, int. 240*
*Skype: panos_mou*

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