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-boun...@r-project.org> on behalf of Leonardo Collado Torres <lcollado...@gmail.com> Sent: Tuesday, January 21, 2020 1:19 PM To: Martin Morgan <mtmorgan.b...@gmail.com> Cc: Zach Shao <zach.s...@gmail.com>; bioc-devel@r-project.org <bioc-devel@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.b...@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-boun...@r-project.org on behalf of zach.s...@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@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@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. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
