[Bioc-devel] Custom build of packages

[Kasper Daniel Hansen]

1. To Ruiz: right now there are tons of changes happening all the time
because we are close to a release.  So what you're asking is much harder
than what you think it is.  Basically, it'll not happen.  What you first
and foremost need to do, is to setup a build on your local machine (which
is seems you have done).  That will help you with many, many problems - but
not problems which are package specific.

2. To others: I do agree that having preconfigured VMs for specific
platforms would be very worthwhile, especially for Windows, as we have just
seen with mzR.  But it would also take effort and there may be licensing
issues related to having an OS ready for download (especially on Windows).
I am not up to date on the docker efforts, perhaps that is the way to go
(but I don't know if that'll help us on Windows).  Perhaps having a
detailed discussion with potential solutions will help us understand to
what extend it is possible and how much effort it requires.

On Fri, Apr 22, 2016 at 9:42 AM, Ruiz Arenas, Carlos <cruiz at creal.cat>
wrote:

> Thanks Leonardo and Steffen,
>
> I have just realized that Martin also mentioned travis in his reply but I
> didn't know what he was talking about. I will try it.
>
> Thank you again,
>
> Carlos Ruiz
>
> ----- Mensaje original -----
> De: "Leonardo Collado Torres" <lcollado at jhu.edu>
> Para: "Steffen Neumann" <sneumann at ipb-halle.de>
> CC: "Martin Morgan" <Martin.Morgan at roswellpark.org>, "Ruiz Arenas,
> Carlos" <cruiz at creal.cat>, bioc-devel at r-project.org
> Enviados: Viernes, 22 de Abril 2016 15:16:27
> Asunto: Re: [Bioc-devel] Custom build of packages
>
> You could also run tests on Travis CI. That's what I do for my
> packages. See https://travis-ci.org/lcolladotor/derfinder and
> https://github.com/lcolladotor/derfinder/blob/master/.travis.yml for
> an example. If you want to use Travis, check the main docs
> https://docs.travis-ci.com/user/languages/r
>
> On Fri, Apr 22, 2016 at 7:59 AM, Steffen Neumann <sneumann at ipb-halle.de>
> wrote:
> > Hi,
> >
> > On Fr, 2016-04-22 at 10:53 +0000, Morgan, Martin wrote:
> >> All packages are built nightly, in both release and devel, and across
> >> three architectures. The build system is more complicated than
> >> building individual packages -- reverse dependencies need to be
> >> built, too, and successful builds synchronized with public
> >> repositories -- so the nightly builds will not change in the near
> >> future.
> >>
> >> The problem is likely that your local configuration is using the
> >> current version of R and Bioconductor, whereas as a developer you
> >> should be using the version of R and Bioconductor used in the 'devel'
> >> branch. The version of R in use on the build machines is given at the
> >> top of the build page
> >
> > I too have wanted the different build environments
> > as close to the "official" BioC machines as possible
> > for debugging. Especially preconfigured VMs or docker images
> > would be great.
> >
> > For the latter, you can use
> >
> >         docker run -ti bioconductor/devel_base bash
> >
> > but I think even that is a slightly different setup
> > compared to the official build animals.
> >
> > I wouldn't even mind if I have to pay amazon (or google or whoever)
> > a few $$$ to fire-up a clone of the build machines,
> > log in remotely, and have a clone of the official environment.
> > Bonus points if that covered windows, mac and Linux alike.
> >
> > Just my 2c,
> > Yours,
> > Steffen
> >
> >
> >
> >
> > --
> > IPB Halle                    AG Massenspektrometrie & Bioinformatik
> > Dr. Steffen Neumann          http://www.IPB-Halle.DE
> > Weinberg 3                   http://msbi.bic-gh.de
> > 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
> >                                   +49 (0) 345 5582 - 0
> > sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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