[Bioc-devel] To Push or Not To Push?

Hervé Pagès hp@ge@ @end|ng |rom |redhutch@org
Sun Apr 26 05:25:25 CEST 2020

Hi Chris,

That is the question :-)

The last run of the builds got delayed (that's because we updated R to 
final 4.0.0 on all build machines on Friday) so we weren't able to 
update the report in time today with the results of the builds. Today's 
builds have started already and I see that CoreGx is on the build 
machines. So if everything goes as expected it should show up on 
tomorrow's report.

I would say push your updates to PharmacoGx. HOWEVER, it's important 
that you run R CMD build/check on PharmacoGx before you do so. Make sure 
you use R 4.0.0 when you do this, that all your packages are up-to-date 
(BiocManager::valid() will tell you that), and that you are using the 
same version of CoreGx that is currently on the build machines (which is 
the one at 'git clone https://git.bioconductor.org/packages/CoreGx'). If 
every looks good then you can push with confidence.

Since today's builds have already started they won't pick up your 
changes to PharmacoGx. But tomorrow's builds will. This means that you 
won't be able to see the full picture before Monday's report. So yes, 
that's kind of last minute but, again, if you're cautious before 
pushing, everything should be fine ;-)


On 4/25/20 17:27, Chris Eeles wrote:
> Hello Bioc-Devel community,
> We recently submitted CoreGx to Bioconductor and am happy to announce it was accepted. However, the package has not yet made it into the 3.11 build and we are concerned it may not make the release.
> Our existing Bioconductor package, PharmacoGx, has significant updates which depend on CoreGx; thus we are hesitant to push our updates without CoreGx being available in 3.11.
> I wonder if anyone can provide guidance on how best to move forward? We would very much like to get the updated PharmacoGx into this release, but don't want to risk releasing a package without a dependency. Should we push and hope for the best or wait until tomorrow to see if we make the final build?
> Any advice would be appreciated.
> Thanks for your support.
> Best,
> ---
> Christopher Eeles
> Software Developer
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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