[Bioc-devel] Error unable to find image

[Leonardo Collado Torres]

Will do, thanks Lori!

Best,
Leo

On Tue, Jan 21, 2020 at 1:24 PM Shepherd, Lori <
Lori.Shepherd using roswellpark.org> wrote:

> Wait for knitr to be available on CRAN.
>
> The builders do not respect remotes to github repos.
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------------------------------
> *From:* Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of
> Leonardo Collado Torres <lcolladotor using gmail.com>
> *Sent:* Tuesday, January 21, 2020 1:19 PM
> *To:* Martin Morgan <mtmorgan.bioc using gmail.com>
> *Cc:* Zach Shao <zach.shao using gmail.com>; bioc-devel using r-project.org <
> bioc-devel using r-project.org>
> *Subject:* Re: [Bioc-devel] Error unable to find image
>
> Hi,
>
> Thanks for the links!
>
> Should we wait for the knitr fix to be available through CRAN or edit our
> DESCRIPTION files to force the Bioc machines to install `knitr` from
> GitHub?
>
> Best,
> Leo
>
> On Mon, Jan 20, 2020 at 12:11 PM Martin Morgan <mtmorgan.bioc using gmail.com>
> wrote:
>
> > This seems to be a problem with a recent change to knitr
> >
> >   https://github.com/Bioconductor/BiocStyle/issues/71
> >   https://github.com/yihui/knitr/issues/1797
> >
> > Please follow these issues; it looks like it is fixed in the github
> > repository, but needs to be made available in CRAN for this to be fixed
> on
> > our build systems.
> >
> > Martin
> >
> > On 1/20/20, 12:00 PM, "Bioc-devel on behalf of Zach Shao" <
> > bioc-devel-bounces using r-project.org on behalf of zach.shao using gmail.com>
> wrote:
> >
> >     Hello,
> >
> >     Not sure what to make of this error
> >
> >     with building the vingette by bioconductor.
> >
> >     The figures are all there.
> >
> >     Did something change with knitr?
> >
> >     Thank you.
> >
> >
> >     Zach
> >
> >
> >
> ##############################################################################
> >
> >
> ##############################################################################
> >     ###
> >     ### Running command:
> >     ###
> >     ###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD build
> >     --keep-empty-dirs --no-resave-data ERSSA
> >     ###
> >
> >
> ##############################################################################
> >
> >
> ##############################################################################
> >
> >
> >     * checking for file ‘ERSSA/DESCRIPTION’ ... OK
> >     * preparing ‘ERSSA’:
> >     * checking DESCRIPTION meta-information ... OK
> >     * installing the package to build vignettes
> >     * creating vignettes ... ERROR
> >     --- re-building ‘ERSSA.Rmd’ using rmarkdown
> >     Quitting from lines 45-46 (ERSSA.Rmd)
> >     Error: processing vignette 'ERSSA.Rmd' failed with diagnostics:
> >     Magick: unable to open image
> >
> >
> `/tmp/Rtmp9aQlKg/Rbuild6d1427846a56/ERSSA/vignettes/ERSSA_files/figure-html/unnamed-chunk-2-1.png':
> >     No such file or directory @ error/blob.c/OpenBlob/2701
> >     --- failed re-building ‘ERSSA.Rmd’
> >
> >     SUMMARY: processing the following file failed:
> >       ‘ERSSA.Rmd’
> >
> >     Error: Vignette re-building failed.
> >     Execution halted
> >
> >         [[alternative HTML version deleted]]
> >
> >     _______________________________________________
> >     Bioc-devel using r-project.org mailing list
> >     https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>         [[alternative HTML version deleted]]
>
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