[Bioc-devel] 'tokay1' error but passed other OS
th@t|kond@92 @end|ng |rom gm@||@com
Wed Sep 4 21:11:56 CEST 2019
@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
@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.
On Wed, Sep 4, 2019 at 8:50 PM Kasper Daniel Hansen <
kasperdanielhansen using gmail.com> wrote:
> 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,
>> of the tools we have for reading BigWig (tracklayer) does not work
>> 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,
>> at least its not Kent tools.
>> On Wed, Sep 4, 2019 at 11:45 AM Venu Thatikonda <thatikonda92 using gmail.com>
>> > 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
>> > 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]]
>> > _______________________________________________
>> > Bioc-devel using r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> [[alternative HTML version deleted]]
>> Bioc-devel using r-project.org mailing list
>> 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.
[[alternative HTML version deleted]]
More information about the Bioc-devel