[Bioc-devel] Custom build of packages

Ruiz Arenas, Carlos cruiz at creal.cat
Fri Apr 22 15:42:42 CEST 2016

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

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
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