[Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

[Dan Tenenbaum]

Attention package maintainers,

When building an R package, if R thinks there is a vignette, it will emit this line during R CMD build:

* creating vignettes ... OK

If there is either no vignette, or in the case of non-sweave vignettes, something is not set up correctly (there are many things that can go wrong), you won't see that line of output. 

This means your vignette will not be available on our web site, nor to end users who install your package.

So going to the build system and looking through all R CMD build output to see which output files do NOT have that line, returns 49 matches:

$ grep -L "creating vignettes ..." *.buildsrc-out.txt 
a4Base.buildsrc-out.txt
a4Classif.buildsrc-out.txt
a4Core.buildsrc-out.txt
a4Preproc.buildsrc-out.txt
a4Reporting.buildsrc-out.txt
affxparser.buildsrc-out.txt
affyio.buildsrc-out.txt
AffyTiling.buildsrc-out.txt
aroma.light.buildsrc-out.txt
arrayQuality.buildsrc-out.txt
bigmemoryExtras.buildsrc-out.txt
BiocCaseStudies.buildsrc-out.txt
BiocGenerics.buildsrc-out.txt
BiocInstaller.buildsrc-out.txt
BufferedMatrixMethods.buildsrc-out.txt
canceR.buildsrc-out.txt
CGHbase.buildsrc-out.txt
CoCiteStats.buildsrc-out.txt
daMA.buildsrc-out.txt
dcGSA.buildsrc-out.txt
DynDoc.buildsrc-out.txt
ExperimentHub.buildsrc-out.txt
flipflop.buildsrc-out.txt
GraphAT.buildsrc-out.txt
HDF5Array.buildsrc-out.txt
hypergraph.buildsrc-out.txt
Icens.buildsrc-out.txt
impute.buildsrc-out.txt
mcaGUI.buildsrc-out.txt
microRNA.buildsrc-out.txt
minet.buildsrc-out.txt
MSstats.buildsrc-out.txt
multtest.buildsrc-out.txt
netresponse.buildsrc-out.txt
nondetects.buildsrc-out.txt
normalize450K.buildsrc-out.txt
oligoClasses.buildsrc-out.txt
parglms.buildsrc-out.txt
plier.buildsrc-out.txt
preprocessCore.buildsrc-out.txt
ProtGenerics.buildsrc-out.txt
QUALIFIER.buildsrc-out.txt
RPA.buildsrc-out.txt
scde.buildsrc-out.txt
seqplots.buildsrc-out.txt
SJava.buildsrc-out.txt
spotSegmentation.buildsrc-out.txt
stepNorm.buildsrc-out.txt
XVector.buildsrc-out.txt

Some of these (a4Base, a4Classif and many more) just have no vignettes/ directory so no vignettes at all.


Others (ExperimentHub for example) have an empty vignettes directory.

But others (QUALIFIER for example) have a vignettes directory with vignette files.

If any packages you maintain do not have a vignette, please add one.

If your package has a vignette in the vignettes/ directory but is in the above list, then you need to fix it.

This page is a good place to start tracking down the problem:

http://yihui.name/knitr/demo/vignette/

For non-sweave (usually knitr) vignettes, the important things to check are:

- knitr should be in the Suggests field in DESCRIPTION
  (if using BiocStyle with rmarkdown, be sure BiocStyle and rmarkdown are
  also in Suggests).
- VignetteBuilder: knitr should be in DESCRIPTION
- The actual vignette file should have a %\VignetteEngine line; see link above
  for more information.

How can you tell if you've fixed the problem? 
run R CMD build on your package and look for the line

* creating vignettes ... OK

In the output. If you don't see that line, your vignette has not been built.

If you've tried all these things and are still running into problems, contact bioc-devel.

Dan