[Bioc-devel] 'tokay1' error but passed other OS

[Kasper Daniel Hansen]

Thanks

My experience with rtracklayer, bigwig and windows is indeed on some
windows machines it works, and others it don't. Not sure what the deciding
factor is, but if it is truly 32 vs 64 bit, that's interesiting

On Wed, Sep 4, 2019 at 1:51 PM Shepherd, Lori <Lori.Shepherd using roswellpark.org>
wrote:

> I looked into this more on our builders.  The examples run fine on 64
> bit.  This seems to be caused by a 32-bit Windows specific ERROR from the
> rtracklayer summary() function for BigWigFile objects.
>
> I will open an issue with rtracklayer (when I can come up with a minimal
> reproducible example) and will post the issue link in your open issue on
> the Contributions tracker to also monitor.
>
>
> In the meantime you could add a file  .BBSoptions that contains the line
> UnsupportedPlatforms: win32  to get an accurate build report and avoid
> building on the 32 bit window until the issue is resolved.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------------------------------
> *From:* Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Kasper
> Daniel Hansen <kasperdanielhansen using gmail.com>
> *Sent:* Wednesday, September 4, 2019 1:41:28 PM
> *To:* Venu Thatikonda <thatikonda92 using gmail.com>
> *Cc:* bioc-devel <bioc-devel using r-project.org>
> *Subject:* Re: [Bioc-devel] 'tokay1' error but passed other OS
>
> Well, yes, its the status on the build system which matters.
>
> In your case it looks like you're doing BigWig parsing. Unfortunately, some
> of the tools we have for reading BigWig (tracklayer) does not work reliably
> on Windows - sometimes it works, sometimes it doesn't. My _guess_ is that
> you're running into this.
>
> It would be great to get this fixed, although that is not your package's
> issue.  One possible alternative is https://github.com/dpryan79/libBigWig
> which Brent Peterson recommends. I don't know if that works on Windows, but
> at least its not Kent tools.
>
> Best,
> Kasper
>
> On Wed, Sep 4, 2019 at 11:45 AM Venu Thatikonda <thatikonda92 using gmail.com>
> wrote:
>
> > Hi,
> >
> > One of my packages during the review is giving an error in bioc windows
> > system. When I build and check from my side in a windows system, there is
> > no error.
> >
> > It's been over a week, not sure what's happening? Should I do something
> > from my side?
> >
> > Bioc issue: https://github.com/Bioconductor/Contributions/issues/1215
> >
> > Build report:
> > http://bioconductor.org/spb_reports/ALPS_buildreport_20190827110407.html
> >
> > Any update/suggestions would be helpful.
> >
> > Thank you.
> >
> > --
> > Best regards
> > Venu Thatikonda
> > https://itsvenu.github.io/
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
> --
> Best,
> Kasper
>
>         [[alternative HTML version deleted]]
>
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-- 
Best,
Kasper

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