[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 at 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 at r-project.org> on behalf of Leonardo Collado Torres <lcolladotor at gmail.com> *Sent:* Tuesday, January 21, 2020 1:19 PM *To:* Martin Morgan <mtmorgan.bioc at gmail.com> *Cc:* Zach Shao <zach.shao at gmail.com>; bioc-devel at r-project.org < bioc-devel at 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 at 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 at r-project.org on behalf of zach.shao at 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
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