[Bioc-devel] reproducing the BioC package error
Hello all, I am trying to reproduce the build error of my package https://master.bioconductor.org/checkResults/3.13/bioc-LATEST/ALPS/nebbiolo1-buildsrc.html As I understand, BioC 3.13 uses R 4.1. However, it seems R 4.1.0 is not yet officially released. Are other developers just downloading the R 4.1.0 devel version and testing their packages? Thank you & stay safe! -- 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
[Bioc-devel] merge github + bioc versions
Hello all, I am a bit confused by how git works with bioc ecosystem. I am following this guide to sync my github + bioc repos (for the first time). https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ After step-6, I see following branches * master remotes/origin/HEAD -> origin/master remotes/origin/master remotes/upstream/RELEASE_3_10 remotes/upstream/master So, if I add new features to the package and commit & push to master branch, does it affect current version that is released in bioc10? Or do they go to bioc11 devel branch and generate build reports, without affecting the package in bioc10? Should I create a branch RELEASE_3_11 and commit all changes to this branch? I want the changes to be released in bioc11 and do not want to affect bioc10 version. Thank you & have a nice day! -- 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
Re: [Bioc-devel] 'tokay1' error but passed other OS
@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 >> *Sent:* Wednesday, September 4, 2019 3:11:56 PM >> *To:* Kasper Daniel Hansen >> *Cc:* Shepherd, Lori ; 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 on behalf of >>>> Kasper Daniel Hansen >>>> *Sent:* Wednesday, September 4, 2019 1:41:28 PM >>>> *To:* Venu Thatikonda >>>> *Cc:* bioc-devel >>>> *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, >>&
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 on behalf of >> Kasper Daniel Hansen >> *Sent:* Wednesday, September 4, 2019 1:41:28 PM >> *To:* Venu Thatikonda >> *Cc:* bioc-devel >> *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 >> 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/ [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] 'tokay1' error but passed other OS
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
[Bioc-devel] Error: DLL 'rgl' not found: maybe not installed for this architecture?
Hi, During one of my R packages bioc review, I see the following 2 errors, one: Error in library.dynam(dynlib, pkg, lib) : DLL 'rgl' not found: maybe not installed for this architecture? Error: .onLoad failed in loadNamespace() for 'rgl', details: call: NULL error:Loading rgl's DLL failed. Execution halted ERROR: lazy loading failed for package 'ALPS' * removing 'C:/Users/pkgbuild/packagebuilder/workers/jobs/1215/2a61338/ALPS.buildbin-libdir/ALPS' I'm not using any functions from 'rgl', not sure why it is a required dependency. Or is there any key detail am I missing? R CMD build, check BiocCheck are very clean on my system. Two: * ERROR: System Files found that should not be git tracked: ALPS.Rproj Based on this discussion ( https://community.rstudio.com/t/should-rproj-files-be-added-to-gitignore/1269), it is in fact a bit useful not adding PACKAGE.Rproj to .gitignore. Do all bioc packages require adding *Rproj to gitignore? Here is the report, if it's helpful. http://bioconductor.org/spb_reports/ALPS_buildreport_20190823145032.html Thank you & have a ncie day! -- 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
[Bioc-devel] Is magrittr "%>%" acceptable in bioc packages?
Hi, As the title says, is %>% acceptable in bioc packages? With BiocCheck, I get a WARNING that is "Add non-empty \\value sections to the following man pages: man/pipe.Rd". Is it okay even if this warning appears ? `R CMD check` didn't give warnings about it. 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
