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

Thu Sep 5 01:46:24 CEST 2019

On 9/4/19 14:10, Venu Thatikonda wrote:
> @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.

Short answer: The suggestion to run 'R CMD check --force-multiarch' was 
for you so you can reproduce the error.

Long answer: Any Windows system I know from the last 15 years or so can 
run processes in 64-bit or 32-bit mode. As you can see here

   https://cran.r-project.org/bin/windows/base/

the Windows binary for R that is available on CRAN is a 32/64 bit 
binary. This means that it can be run in either mode. You can choose the 
mode in which you want to run R by specifying --arch x64 or --arch i386 
when invoking R. The 64-bit mode is the default so starting R with 'R 
--arch x64' is the same as just starting it with 'R'. The startup 
message tells you if R is running in 64-bit or 32-bit mode.

Now about packages: You can check your package with 'R --arch x64 CMD 
check' (or just 'R CMD check') in which case all the examples and unit 
tests are run in 64-bit mode. If you check your package with 'R --arch 
i386 CMD check' then all the examples and unit tests are run in 32-bit 
mode. If you check your package with 'R CMD check --force-multiarch' 
then all the examples and unit tests are run in both 32-bit and 64-bit. 
This is the recommended way to fully check a package on Windows. Note 
that this is also what our build system does. See for example the 
command used to check the Biobase package on our Windows server tokay1:
https://bioconductor.org/checkResults/3.10/bioc-LATEST/Biobase/tokay1-checksrc.html

AFAIK almost nobody runs R in 32-bit mode on Windows these days so it is 
not a big deal to mark your package as unsupported on 32-bit Windows. 
The only reason we check that packages run fine on 32-bit Windows is 
because we **distribute** Windows binary packages that are also 32/64 
bit binaries (like R itself) and we want to make sure that the bi-arch 
binaries work as expected. And the only reason we distribute these 
Windows bi-arch binaries is because that's what the CRAN folks do.

Hope this helps,

H.

> 
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__aka.ms_ghei36&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=aQi9_aFwkzSWsjF-7jX78IkBFK2Uklnb9lRO4dYLP1g&s=ihotCyW8XeebFWMRpIxoo00e5EKTqdcwK_UDQ_Kc2Sc&e= >
>>>
>>> ------------------------------
>>> *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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dpryan79_libBigWig&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=aQi9_aFwkzSWsjF-7jX78IkBFK2Uklnb9lRO4dYLP1g&s=pBZf3J7V1OUXWtu0-VGofDEljkmQZFxMnOtzTQjSQ4U&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=aQi9_aFwkzSWsjF-7jX78IkBFK2Uklnb9lRO4dYLP1g&s=qcwbOVDWc7xUmkC9JZ2SwXqXS2MKWNgfrxhzTF4TdvQ&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=aQi9_aFwkzSWsjF-7jX78IkBFK2Uklnb9lRO4dYLP1g&s=7K7UpdXrVeKNBEvQrL7SeHFSNkjt_RNGD5N8O5GIgYk&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=aQi9_aFwkzSWsjF-7jX78IkBFK2Uklnb9lRO4dYLP1g&s=bByAo9jgLy3rCGVXBu_j_LLjvMjOs4m8u0myVGgnJDk&e=
>>>>>>
>>>>>>          [[alternative HTML version deleted]]
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel using r-project.org mailing list
>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=aQi9_aFwkzSWsjF-7jX78IkBFK2Uklnb9lRO4dYLP1g&s=2d-f4cnPnfjwQEXB3l9-T8ba6vTDzDi0vNYh0JnywWo&e=
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Best,
>>>>> Kasper
>>>>>
>>>>>          [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel using r-project.org mailing list
>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=aQi9_aFwkzSWsjF-7jX78IkBFK2Uklnb9lRO4dYLP1g&s=2d-f4cnPnfjwQEXB3l9-T8ba6vTDzDi0vNYh0JnywWo&e=
>>>>>
>>>>> This email message may contain legally privileged and/or confidential
>>>>> information. If you are not the intended recipient(s), or the employee or
>>>>> agent responsible for the delivery of this message to the intended
>>>>> recipient(s), you are hereby notified that any disclosure, copying,
>>>>> distribution, or use of this email message is prohibited. If you have
>>>>> received this message in error, please notify the sender immediately by
>>>>> e-mail and delete this email message from your computer. Thank you.
>>>>
>>>>
>>>>
>>>> --
>>>> Best,
>>>> Kasper
>>>>
>>>
>>>
>>> --
>>> Best regards
>>> Venu Thatikonda
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__itsvenu.github.io_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=aQi9_aFwkzSWsjF-7jX78IkBFK2Uklnb9lRO4dYLP1g&s=bByAo9jgLy3rCGVXBu_j_LLjvMjOs4m8u0myVGgnJDk&e=
>>>
>>> This email message may contain legally privileged and/or confidential
>>> information. If you are not the intended recipient(s), or the employee or
>>> agent responsible for the delivery of this message to the intended
>>> recipient(s), you are hereby notified that any disclosure, copying,
>>> distribution, or use of this email message is prohibited. If you have
>>> received this message in error, please notify the sender immediately by
>>> e-mail and delete this email message from your computer. Thank you.
>>
>>
>>
>> --
>> Best,
>> Kasper
>>
> 
> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319