Also be sure you are using a recent version of R-devel. Dan
----- Original Message ----- > From: "Paul Grosu" <pgr...@gmail.com> > To: "Fan, Jean" <jean...@fas.harvard.edu> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Thursday, January 28, 2016 7:49:09 AM > Subject: Re: [Bioc-devel] Vignette building fails > 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
