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

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Wed Sep 4 19:51:54 CEST 2019

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.


On Wed, Sep 4, 2019 at 11:45 AM Venu Thatikonda <thatikonda92 using gmail.com>

> 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


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