Thanks Dan, this solved the problem ! / Leo
On Mon, Sep 15, 2014 at 6:42 PM, Dan Tenenbaum <dtene...@fhcrc.org> wrote: > 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 > > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
