Hi Leo, ----- Original Message ----- > From: "Leo Lahti" <leo.la...@iki.fi> > To: bioc-devel@r-project.org > Sent: Monday, September 15, 2014 10:19:55 AM > Subject: [Bioc-devel] BiocCheck crash with package vignette? > > Dear Bioc developers, > > The BioC guidelines request that package authors run BiocCheck > successfully > before package submission. To get this working in Linux, I copied the > BiocCheck script to /usr/lib/R/bin as adviced and it seemed to work. > However, I am now bumping into problems with BiocCheck related to > vignette. > > Specifically, after successfully building package tarball without > errors/warnings in R version 3.1.1 the BiocCheck generates the > following > error. This error is not solved by adding the argument > --no-check-vignettes > nor by running BiocCheck from R: > > > R CMD BiocCheck -mypackage_0.99.0.tar.gz > > * This is BiocCheck, version 1.0.2. > * BiocCheck is a work in progress. Output and severity of issues may > change. > * Installing package... > * This is a software package, checking vignette directories... > * # of chunks: 4, # of eval=FALSE: 1 (25%) > * Checking version number... > * RECOMMENDED: y of x.y.z version should be even in release > * Checking biocViews... > * Checking build system compatibility... > * Checking unit tests... > Warning in file(filename, "r") : > cannot open file '/tmp/RtmpGXbMdl/vignette.Rmd': No such file or > directory > Error in file(filename, "r") : cannot open the connection > Calls: <Anonymous> ... BiocCheck -> parseFiles -> parseFile -> parse > -> file > Execution halted > > > My package contains the file vignettes/vignette.Rmd and I can convert > this > with knitr without problems. I have not been able solve this after > considerable searching of hints from the web. > > Any ideas on what is causing this failure, and how to solve it ? > > The source code for my problematic package is here, if it is of any > help: > https://github.com/microbiome/microbiome/ >
This is a bug in BiocCheck, it's trying to figure out how to extract the R code from your vignette and since it didn't find VignetteBuilder: knitr in your DESCRIPTION file, it tries to Stangle a non-existent .Rnw file. I'll fix this but you can avoid the problem by adding VignetteBuilder: knitr to your DESCRIPTION file. Perhaps BiocCheck can detect this situation as well. Dan > best regards > Leo Lahti > > [[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
