[Bioc-devel] Error unable to find image

[Leonardo Collado Torres]

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]]
>
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