[Bioc-devel] BiocCheck crash with package vignette?

Leo Lahti leo.lahti at iki.fi
Mon Sep 15 19:19:55 CEST 2014

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
* 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:

best regards
Leo Lahti

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