[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 at 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 at 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 at r-project.org> on behalf of Kasper Daniel Hansen <kasperdanielhansen at gmail.com> *Sent:* Wednesday, September 4, 2019 1:41:28 PM *To:* Venu Thatikonda <thatikonda92 at gmail.com> *Cc:* bioc-devel <bioc-devel at 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 <thatikonda92 at 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:
Any update/suggestions would be helpful. Thank you. -- Best regards Venu Thatikonda https://itsvenu.github.io/ [[alternative HTML version deleted]]
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--
Best,
Kasper
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Best regards Venu Thatikonda https://itsvenu.github.io/ [[alternative HTML version deleted]]