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

Wed Sep 4 23:10:02 CEST 2019

@Lori, sure. I will open the issue with an example.

@Daniel, I didn't understand, I thought this suggestion is for Lori (?).

Do I need to run `R CMD check --force-multiarch` on a windows 32bit system
from my side? If that's the case, It won't be practical from my side,
because I have to borrow someone's system who is using win32. If not, I ran
it on macOS with '--force-multiarch' and it's clean. Except one note about
'.BBSoptions' file, I guess it's okay? Any clarifications would be
appreciated.

Thank you.

On Wed, Sep 4, 2019 at 9:38 PM Kasper Daniel Hansen <
kasperdanielhansen using gmail.com> wrote:

> 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/
>>
>> This email message may contain legally privileged and/or confidential
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>
>
> --
> Best,
> Kasper
>

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

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