----- Original Message ----- > From: "Karim Mezhoud" <kmezh...@gmail.com> > To: "bioc-devel" <bioc-devel@r-project.org> > Cc: "Dan Tenenbaum" <dtene...@fredhutch.org> > Sent: Tuesday, March 29, 2016 6:11:15 AM > Subject: Re: [Bioc-devel] 49 software packages either have no vignettes or > their vignettes are not built by R CMD build!
> 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. That is not a problem. However, your vignette is not built during R CMD build. Looks like the problem is you are missing the following in DESCRIPTION: Suggests: R.rsp VignetteBuilder: R.rsp See https://cran.r-project.org/web/packages/R.rsp/vignettes/R_packages-LaTeX_vignettes.pdf . > > 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 Are you using the command line or some kind of gui interface to git? Try using the command line.A > > 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? > You cannot, the repositories in bioc-mirror are read-only. Dan > 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
