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 g...@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 <hpa...@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.fhcrc.org/bioconductor/trunk/madman/Rpacks/metaseqR@129129
bc3139a8-67e5-0310-9ffc-ced21a209358
Martin
Any suggestions are most welcome. Thanks in advance.
Panagiotis
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