[Bioc-devel] Wishlist: on demand R CMD check

[Kasper Daniel Hansen]

I was not envisioning a "proper" check, merely running R CMD check with the
current version on the build system of all packages (latest R CMD check).
Somehow I imagine we have an R with all of Bioc installed as per a certain
check date, although this might not be what is actually happening.

So this would not handle the situation where I want to check package B
which depends on package A which I just updated.  This does happen, but (at
least for me) much less frequently than "I am tracking down some bug
somwhere (perhaps introduced elsewhere).

Like I said, for many problems I can do this well on my machine.  But
sometimes I can't.

Best,
Kasper

On Tue, Jun 2, 2015 at 8:39 AM, Laurent Gatto <lg390 at cam.ac.uk> wrote:

>
> To what extend could the single package builder be used for such a
> feature? This would not address Michael's point, but it is a way to get
> access to all archs using existing software infrastructure.
>
> Laurent
>
> On  2 June 2015 13:18, Michael Lawrence wrote:
>
> > Maybe the motion towards github and the work Gabor C has been doing on
> > Travis integration might help with this?
> >
> > Note that a proper check should test all reverse dependencies of your
> > package, and that would get expensive for some of the more core
> > packages... so that might need to be deferred to the regular
> > repository-level build process.
> >
> >
> > On Tue, Jun 2, 2015 at 2:48 AM, Sean Davis <seandavi at gmail.com> wrote:
> >> On Tue, Jun 2, 2015 at 5:32 AM, Vincent Carey <
> stvjc at channing.harvard.edu>
> >> wrote:
> >>
> >>> I agree that this would be nice; not sure how feasible.  Could a
> specific
> >>> approach with containers provide a solution?
> >>>
> >>
> >> Unfortunately, containers are linux microkernels, so Windows and MacOS
> are
> >> basically out.
> >>
> >>
> >>> On Mon, Jun 1, 2015 at 11:09 PM, Kasper Daniel Hansen <
> >>> kasperdanielhansen at gmail.com> wrote:
> >>>
> >>> > For a substantial number of issues with R CMD check, it is easy to
> >>> > reproduce the errors/warnings/notes on my own system; simply update
> all
> >>> > packages and run the test.
> >>> >
> >>> > For a small number of errors I have sometimes (over the years) had
> >>> problems
> >>> > reproducing them, perhaps because they are platform specific or
> because
> >>> of
> >>> > other issues.
> >>> >
> >>> > In those cases, especially for packages which I work on
> infrequently, the
> >>> > current submission / check introduces a long delay and - more
> >>> importantly -
> >>> > substantial mental overhead for me.  This is because I submit a fix
> and
> >>> > then I usually have to wait 36-48h to see the result of R CMD check.
> >>> >
> >>> > It would be great if we could get access to running R CMD check on
> all
> >>> > three platforms by demand, with a results page which is semi-private
> (to
> >>> > not confuse the package with a fix with the official devel
> version).  I
> >>> > realize this could be misused or introduce a large computational
> overhead
> >>> > on the project.  Perhaps only make this available for packages
> accepted
> >>> > into the project.  But it would be nice.  For example, I have been
> >>> hunting
> >>> > a bug in minfi for like 10 days now, and the fact that I need to
> wait 48h
> >>> > to get the result of a fix, really makes this painful.
> >>> >
> >>> > Best,
> >>> > Kasper
> >>> >
> >>> >         [[alternative HTML version deleted]]
> >>> >
> >>> > _______________________________________________
> >>> > Bioc-devel at r-project.org mailing list
> >>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>> >
> >>>
> >>>         [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> Bioc-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>
> >>         [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> --
> Laurent Gatto | @lgatt0
> http://cpu.sysbiol.cam.ac.uk/
>
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>

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