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

[Venu Thatikonda]

@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> 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> 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
>


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

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