Will do, thanks Lori! Best, Leo
On Tue, Jan 21, 2020 at 1:24 PM Shepherd, Lori < lori.sheph...@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-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