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

[Shepherd, Lori]

Venu,
If you can produce a minimal example that can reproduce it and open the issue on rtracklayer github that would be great.  Please tag me when you do so I can keep track of it also @lshep on GitHub
Cheers

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________________________________
From: Venu Thatikonda <thatikonda92 using gmail.com>
Sent: Wednesday, September 4, 2019 3:11:56 PM
To: Kasper Daniel Hansen <kasperdanielhansen using gmail.com>
Cc: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>; bioc-devel <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] 'tokay1' error but passed other OS

@Daniel, I guess using libBigWig cause even more problems while build, check commands as this is an non R library. But I'm not sure if this works out.

@Lori, Thanks a lot for looking into the error. Interesting to see what's missing from win32. I will add the .BBSoptions file and bump the version as suggested. I can create a small example to reproduce the error(?), to open an issue at rtracklayer, please let me know if that's okay.

Thank you.

On Wed, Sep 4, 2019 at 8:50 PM Kasper Daniel Hansen <kasperdanielhansen using gmail.com<mailto:kasperdanielhansen using gmail.com>> wrote:
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<mailto: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<mailto:bioc-devel-bounces using r-project.org>> on behalf of Kasper Daniel Hansen <kasperdanielhansen using gmail.com<mailto:kasperdanielhansen using gmail.com>>
Sent: Wednesday, September 4, 2019 1:41:28 PM
To: Venu Thatikonda <thatikonda92 using gmail.com<mailto:thatikonda92 using gmail.com>>
Cc: bioc-devel <bioc-devel using r-project.org<mailto: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<mailto: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/
>
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>
> _______________________________________________
> Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


--
Best,
Kasper

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Best,
Kasper


--
Best regards
Venu Thatikonda
https://itsvenu.github.io/


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