Hi Jean, I think you might need to update the required packages, so that they install if you don't have them installed. The test I usually run is by keeping clean R installations and testing packages fresh as if I am a user who just downloaded R. You seem to need org.Hs.eg.db and GO.db for the vignette, which I'm not sure the package automatically downloads, but those can take some time.
And as always feel free to check with folks on this list :) Hope it helps, `p On Thu, Jan 28, 2016 at 9:44 AM, Fan, Jean <jean...@fas.harvard.edu> wrote: > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
