Hi Martin, Ah, I didn’t realize the problems were connected. Yes, the vignettes do take quite a while to run. I’ll see what I can do. Thanks for the help.
Best, Jean > On Jan 28, 2016, at 9:28 AM, Morgan, Martin <martin.mor...@roswellpark.org> > wrote: > > I tried to build your vignettes on my own computer, but they are taking too > long. From > > http://bioconductor.org/developers/package-guidelines/#correctness > > the time limit for checking a package (which includes running the vignette > code, though not building the vignette) is 5 minutes. Do your vignettes take > a lot of time to build? > > If so, you should first identify the slow portion of your code and attempt to > vectorize it; ask here for help if needed. > > You should then construct examples for use in your vignette that are > sufficiently realistic to shine a favorable light on the full richness of > your software, but easily computed within the available time. > > Martin > > ________________________________________ > From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Fan, Jean > <jean...@fas.harvard.edu> > Sent: Thursday, January 28, 2016 8:37 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] Vignette building fails > > Hello, > > I recently updated my bioconductor package via svn. The package was built > successfully on my computer via R CMD build scde and passed R CMD check scde > and R CMD BiocCheck scde. But the build report on Bioconductor ran into the > following errors when building the vignettes: > > * checking for file ‘scde/DESCRIPTION’ ... OK > * preparing ‘scde’: > * checking DESCRIPTION meta-information ... OK > * cleaning src > * installing the package to build vignettes > * creating vignettes ... ERROR > Loading required package: flexmix > Loading required package: lattice > Error: processing vignette 'diffexp.Rmd' failed with diagnostics: > Failed to locate the ‘weave’ output file (by engine ‘knitr::rmarkdown’) for > vignette with name ‘diffexp’. The following files exist in directory ‘.’: > ‘diffexp.R’, ‘diffexp.Rmd’, ‘diffexp.md’, ‘pagoda.Rmd’ > Execution halted > > I was able to build the vignettes locally using R CMD Sweave so I’m not sure > what’s wrong. I haven’t been able to find any solutions by Googling around. > Has anyone else encountered this error before? > > Thanks, > Jean > > Jean Fan > PhD Candidate > NSF GRFP > Kharchenko Lab > Harvard University > 10 Shattuck St #3, Countway 336B > Boston, MA 02115 > > [[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. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
