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

[Kasper Daniel Hansen]

Venu, you should really follow Herve's suggestion and use R CMD check
--force-multiarch and report back the result.

On Wed, Sep 4, 2019 at 3:32 PM Shepherd, Lori <Lori.Shepherd using roswellpark.org>
wrote:

> 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
>
> Get Outlook for Android <https://aka.ms/ghei36>
>
> ------------------------------
> *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> 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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-- 
Best,
Kasper

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