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

[Karim Mezhoud]

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 <dtenenba at fredhutch.org>
wrote:

>
>
> ----- Original Message -----
> > From: "Karim Mezhoud" <kmezhoud at gmail.com>
> > To: "bioc-devel" <bioc-devel at r-project.org>
> > Cc: "Dan Tenenbaum" <dtenenba at 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 <dtenenba at 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 at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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