@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 < 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://aka.ms/ghei36> >> >> ------------------------------ >> *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://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 <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://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@r-project.org mailing list >>>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>> > >>>> >>>> >>>> -- >>>> Best, >>>> Kasper >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>> >>>> 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://itsvenu.github.io/ >> >> 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://itsvenu.github.io/ [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
