Thank you, I am in devel branch (git checkout devel) . when I "git svn rebase" I get all changed files with message: needs update. How can I update. km
On Tue, Mar 29, 2016 at 4:16 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > > > ----- 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. > > > > 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. > > > > It sounds like you already had a github repository before the fork. In > this case, do not fork, just run the update_remotes.sh script. > Dan > > > > 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
