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 < > kasperdanielhan...@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.sheph...@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 <thatikond...@gmail.com> >>> *Sent:* Wednesday, September 4, 2019 3:11:56 PM >>> *To:* Kasper Daniel Hansen <kasperdanielhan...@gmail.com> >>> *Cc:* Shepherd, Lori <lori.sheph...@roswellpark.org>; bioc-devel < >>> bioc-devel@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 < >>> kasperdanielhan...@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.sheph...@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-boun...@r-project.org> on behalf of >>>>> Kasper Daniel Hansen <kasperdanielhan...@gmail.com> >>>>> *Sent:* Wednesday, September 4, 2019 1:41:28 PM >>>>> *To:* Venu Thatikonda <thatikond...@gmail.com> >>>>> *Cc:* bioc-devel <bioc-devel@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 <thatikond...@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@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@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: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel