[Bioc-devel] Fwd: TissueEnrich problems reported in the Multiple platform build/check report for BioC 3.9

Ashish Jain j@|n @end|ng |rom |@@t@te@edu
Tue Sep 17 18:17:27 CEST 2019


Hi Lori,

Thank you for your help. I was able to reproduce the issue locally after
updating the packages. I updated the vignette with the changes and pushed
it on both RELEASE_3_9 and the development (3_10) branches. Again thank you
for your help!

Regards,
Ashish Jain

On Tue, Sep 17, 2019 at 7:06 AM Shepherd, Lori <
Lori.Shepherd using roswellpark.org> wrote:

> I am able to reproduce the ERROR.  It seems to be an issue of trying to
> subset.
>
> > head(exp %>% gather(Tissue))          Tissue             value
> 1 Adipose Tissue  1.63226821549951
> 2 Adipose Tissue                 0
> 3 Adipose Tissue                 0
> 4 Adipose Tissue 0.485426827170242
> 5 Adipose Tissue 0.584962500721156
> 6 Adipose Tissue  3.05311133645956> head(exp %>% gather(Tissue=1:(ncol(exp)-1)))Error: 1 components of `...` had unexpected names.
>
> We detected these problematic arguments:
> * `Tissue`
>
> Did you misspecify an argument?Call `rlang::last_error()` to see a backtrace
>
> >
>
> You can see if there were any recent changes to package you depend on that
> could have caused this.  A package you depend on may have changed their
> functionality.  I needed to update packages (with BiocManager::install()
>  update all )  in order to reproduce.
>
> Cheers,
>
> 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 Ashish
> Jain <jain using iastate.edu>
> *Sent:* Monday, September 16, 2019 3:08 PM
> *To:* bioc-devel using r-project.org <bioc-devel using r-project.org>
> *Subject:* [Bioc-devel] Fwd: TissueEnrich problems reported in the
> Multiple platform build/check report for BioC 3.9
>
> Hi All,
>
> I just got the message that my package is giving an error during the build
> process on Bioconductor build server. I saw the logs and found it is
> failing while building the vignette. I am not sure why it's happening as I
> have not updated the package since release and it was building without any
> errors. Can someone look into this?
>
> Regards,
> Ashish Jain
>
> ---------- Forwarded message ---------
> From: <BBS-noreply using bioconductor.org>
> Date: Mon, Sep 16, 2019 at 1:59 PM
> Subject: TissueEnrich problems reported in the Multiple platform
> build/check report for BioC 3.9
> To: <jain using iastate.edu>
>
>
> [This is an automatically generated email. Please don't reply.]
>
> Hi TissueEnrich maintainer,
>
> According to the Multiple platform build/check report for BioC 3.9,
> the TissueEnrich package has the following problem(s):
>
>   o ERROR for 'R CMD build' on malbec2. See the details here:
>
>
> https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/TissueEnrich/malbec2-buildsrc.html
>
> Please take the time to address this by committing and pushing
> changes to your package at git.bioconductor.org
>
> Notes:
>
>   * This was the status of your package at the time this email was sent to
> you.
>     Given that the online report is updated daily (in normal conditions)
> you
>     could see something different when you visit the URL(s) above,
> especially if
>     you do so several days after you received this email.
>
>   * It is possible that the problems reported in this report are false
> positives,
>     either because another package (from CRAN or Bioconductor) breaks your
>     package (if yours depends on it) or because of a Build System problem.
>     If this is the case, then you can ignore this email.
>
>   * Please check the report again 24h after you've committed your changes
> to the
>     package and make sure that all the problems have gone.
>
>   * If you have questions about this report or need help with the
>     maintenance of your package, please use the Bioc-devel mailing list:
>
>       https://bioconductor.org/help/mailing-list/
>
>     (all package maintainers are requested to subscribe to this list)
>
> For immediate notification of package build status, please
> subscribe to your package's RSS feed. Information is at:
>
> https://bioconductor.org/developers/rss-feeds/
>
> Thanks for contributing to the Bioconductor project!
>
>
>
> --
> Regards,
> Ashish Jain
> Ph.D. Candidate
> Bioinformatics and Computational Biology
> Iowa State University
> Ph +1-317-529-7973
> Website: *https://ashishjain1988.github.io
> <https://ashishjain1988.github.io/>/*
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using 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.



-- 
Regards,
Ashish Jain
Ph.D. Candidate
Bioinformatics and Computational Biology
Iowa State University
Ph +1-317-529-7973
Website: *https://ashishjain1988.github.io
<https://ashishjain1988.github.io/>/*

	[[alternative HTML version deleted]]



More information about the Bioc-devel mailing list