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

[Pages, Herve]

Also note that since the error is specific to 32-bit Windows, you need 
to run 'R CMD check --force-multiarch' on your package source tarball in 
order to reproduce the error. Without the --force-multiarch flag, 'R CMD 
check' only runs the examples and unit tests for the default arch, 
which, for 99.99% of Windows users is the 64-bit arch.

H.


On 9/4/19 10:51, Shepherd, Lori 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dpryan79_libBigWig&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cLVKSXICD34PS8AZqtoyaNp-NKH4jvXvlMjVW8jt_0s&s=ujpFo4P7955D90ROfqBqHGmRhZnyQQXnY-dRu0IrCHg&e=
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_1215&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cLVKSXICD34PS8AZqtoyaNp-NKH4jvXvlMjVW8jt_0s&s=auK8S9mNR1K0mIEc6Dyi8jeHYdf6Ijtzg29zCGvjdRw&e=
>>
>> Build report:
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_spb-5Freports_ALPS-5Fbuildreport-5F20190827110407.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cLVKSXICD34PS8AZqtoyaNp-NKH4jvXvlMjVW8jt_0s&s=j5hCJlgAQJoMHlJFjSemKuaI7vmqAT90vBkVeTmXP5s&e=
>>
>> Any update/suggestions would be helpful.
>>
>> Thank you.
>>
>> --
>> Best regards
>> Venu Thatikonda
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__itsvenu.github.io_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cLVKSXICD34PS8AZqtoyaNp-NKH4jvXvlMjVW8jt_0s&s=6PbKmuIeMjhsNWRno7PAuILcsvVkhURn29ZwDQkuzCY&e=
>>
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>>
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>>
> 
> 
> --
> Best,
> Kasper
> 
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-- 
Hervé Pagès

Program in Computational Biology
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