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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
