Dear Dr Dan, Thank you for this note. In my case (canceR), I am using sweave and having:
checking PDF version of manual ... [8s/19s] OK during R CMD Check. I need to sync devel version using git-mirrors ( https://www.bioconductor.org/developers/how-to/git-mirrors/). I am following scenario 2. When I fork bioc-mirror/canceR I get two repo with the same name in my github. at step 4 of tutorial, I can not push some changes: error: unable to read askpass response from 'rpostback-askpass' fatal: could not read Username for 'https://github.com': Device not configured 1- How can I configure access to bioc-mirror/canceR. 2- What is the utility of the fork if we can commit directly to bioc-mirror/canceR? Thank you Karim On Wed, Mar 23, 2016 at 10:44 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
