On 05/20/2013 02:00 PM, Wolfgang Huber wrote:
I am puzzled by the interpretation of the %\VignetteIndexEntry directive by the
build system. On
http://www.bioconductor.org/packages/devel/bioc/html/genefilter.html of the
four vignettes for this package, two are listed with titles
1. <empy title>
2. Additional plots for: Independent filtering increases power for detecting
differentially expressed genes
whereas in the .Rnw files, these two lines are provided (
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genefilter/inst/doc
)
1. %\VignetteIndexEntry{Diagnostics for independent filtering}
2. %\VignetteIndexEntry{Additional plots for: Independent filtering increases
power for detecting differentially expressed genes, Bourgon et al., PNAS (2010)}
both of these do not match what is rendered (the first more obviously so).
Anybody have an idea what's wrong or how to properly do this?
If I build and install the package from source, and then ask for
`vignette(package="genefilter")` the full content of \VignetteIndexEntry
appears. So I think this is post-processing of the build system; Dan is away
today but will have more information in the near future.
Martin
Best wishes
Wolfgang
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