[Bioc-devel] Error unable to find image

[Shepherd, Lori]

We have actually decided to upload the current github version on the builders manually while we wait for it to get into CRAN so that you can all hopefully get clean builds.  The release builders were updated yesterday and the devel builders are being updated now.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Leonardo Collado Torres <lcolladotor using gmail.com>
Sent: Tuesday, January 21, 2020 3:08 PM
To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Cc: Martin Morgan <mtmorgan.bioc using gmail.com>; 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

Will do, thanks Lori!

Best,
Leo

On Tue, Jan 21, 2020 at 1:24 PM Shepherd, Lori <Lori.Shepherd using roswellpark.org<mailto: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<mailto:bioc-devel-bounces using r-project.org>> on behalf of Leonardo Collado Torres <lcolladotor using gmail.com<mailto:lcolladotor using gmail.com>>
Sent: Tuesday, January 21, 2020 1:19 PM
To: Martin Morgan <mtmorgan.bioc using gmail.com<mailto:mtmorgan.bioc using gmail.com>>
Cc: Zach Shao <zach.shao using gmail.com<mailto:zach.shao using gmail.com>>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto: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<mailto: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<mailto:bioc-devel-bounces using r-project.org> on behalf of zach.shao using gmail.com<mailto: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<mailto:Bioc-devel using r-project.org> mailing list
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>
> _______________________________________________
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>

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