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

Chris Eeles chr|@topher@ee|e@ @end|ng |rom out|ook@com
Sun Apr 26 17:32:42 CEST 2020

Hi Herve,

Thanks for the advice. We have been pretty thorough with our testing, so I think we will do a final check and push today.


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From: Herv� Pag�s <hpages using fredhutch.org>
Sent: Saturday, April 25, 2020 11:25:25 PM
To: Chris Eeles <christopher.eeles using outlook.com>; Bioc-devel using r-project.org <Bioc-devel using r-project.org>
Cc: Smirnov, Petr <Petr.Smirnov using uhnresearch.ca>
Subject: Re: [Bioc-devel] To Push or Not To Push?

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://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.bioconductor.org%2Fpackages%2FCoreGx&data=02%7C01%7C%7Cc60f0240a759498f15d708d7e9917836%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637234683299229138&sdata=qF2Ja1UekdeTjXDUfVR7aDRNY4RbfpsofFhn%2FDOqOAM%3D&reserved=0'). 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
> BHK Laboratory<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.bhklab.ca_%26d%3DDwICAg%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DLa4zNgzQBGQqABiXaILnttyOue2enaUkt_LSHyWgZFY%26s%3D9d3um0IkW59E0g04Fa5xFUEGdh-JKYmp18FB2kBZAVo%26e%3D&data=02%7C01%7C%7Cc60f0240a759498f15d708d7e9917836%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637234683299239127&sdata=jmoPuh3fpo0%2FVRsk%2BdFDcprdjA0k6BA3I1I7XwyYBTY%3D&reserved=0 >
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