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

Martin Morgan martin.morgan at roswellpark.org
Fri Aug 25 12:14:08 CEST 2017

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



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



> Any suggestions are most welcome. Thanks in advance.
> Panagiotis

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