[Bioc-devel] Package "not supported" on some platforms, and dependent packages

[Kevin RUE]

Oh right, Thanks for the clarification Valerie!
Kevin

On Wed, Oct 19, 2016 at 5:09 PM, Obenchain, Valerie <
Valerie.Obenchain at roswellpark.org> wrote:

> Just fyi, as stated in the NEWS, ensemblVEP >= 1.12.0 is not supported
> on windows because the Ensembl VEP tool >= 84 requires tabix.
>
> Valerie
>
>
> On 10/18/2016 04:01 PM, Kevin RUE wrote:
> > Arrrrgh, I could have looked better in the Git mirror code ;)
> >
> > Anyway, thanks a lot for the tip!
> >
> > No worries about removing the file if the parent package gets supported.
> > However, I've never tried to run the VEP script on Windows, which I
> expect
> > is pre-requisite for the package building successfully there. Might not
> be
> > that easy. Anyway, future will tell, and I'll keep an eye out for it!
> >
> > Cheers
> > Kevin
> >
> >
> > On Tue, Oct 18, 2016 at 11:44 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
> > wrote:
> >
> >>
> >> ----- Original Message -----
> >>> From: "Kevin RUE" <kevinrue67 at gmail.com>
> >>> To: "bioc-devel" <bioc-devel at r-project.org>
> >>> Sent: Tuesday, October 18, 2016 3:28:23 PM
> >>> Subject: [Bioc-devel] Package "not supported" on some platforms,
> >> and dependent packages
> >>
> >>> Hi all,
> >>>
> >>> Heartless logic works as follows:
> >>>
> >>>   - ensemblVEP is "not supported" on Windows (build report
> >>>   <http://bioconductor.org/checkResults/devel/bioc-LATEST/ensemblVEP/
> >).
> >>>   Completely understandable.
> >>>   - My package depends on ensemblVEP.
> >>>   - The build system reports an error on Windows for my package
> >>> because "dependency
> >>>   'ensemblVEP' is not available for package 'TVTB'" (build report
> >>>   <http://bioconductor.org/checkResults/devel/bioc-
> >> LATEST/TVTB/tokay2-buildsrc.html>
> >>>   )
> >>>   - As a result, the landing page for my package reports "build error"
> (
> >>>   page <https://www.bioconductor.org/packages/release/bioc/html/
> >> TVTB.html>)
> >>> I was hoping to benefit of the same treatment as the ensemblVEP
> package,
> >>> that is, skipping the nightly build on the Windows machine, to get the
> >> nice
> >>> green light "build OK" on the landing page.
> >>>
> >>> I suppose this is something to control in the build system, right? Or
> do
> >> I
> >>> have to put any kind of keyword in one of my package files?
> >>> Thanks!
> >>>
> >> The build system is heartless. ;)
> >> ensemblVEP is marked as unsupported on Windows by virtue of a
> .BBSoptions
> >> file in the top level (at the same level as DESCRIPTION) containing one
> >> line:
> >>
> >> UnsupportedPlatforms: win
> >>
> >> If you add that to your package it will stop building (and failing) on
> >> windows.
> >>
> >> If ensemblVEP is ever again supported on windows (I don't know if this
> is
> >> planned) you'll need to remove that file.
> >>
> >> Dan
> >>
> >>
> >>> All the best,
> >>> Kevin
> >>>
> >>>       [[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
> >
>
>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>

	[[alternative HTML version deleted]]