'Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R'

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List:       bioc-devel
Subject:    Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R
From:       Dan Tenenbaum <dtenenba () fredhutch ! org>
Date:       2016-03-29 19:12:15
Message-ID: 512847219.3782489.1459278735961.JavaMail.zimbra () fredhutch ! org
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----- Original Message -----
> From: "Karim Mezhoud" <kmezhoud@gmail.com>
> To: "Dan Tenenbaum" <dtenenba@fredhutch.org>
> Cc: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Tuesday, March 29, 2016 12:05:03 PM
> Subject: Re: [Bioc-devel] 49 software packages either have no vignettes or their \
> vignettes are not built by R CMD build!

> Thank you,
> I am in devel branch (git checkout devel) .
> 
> when I "git svn rebase" I get all changed files with message: needs update.

This doesn't happen with me:

clone https://github.com/kmezhoud/canceR.git
cd canceR/
../mirror/update_remotes.sh
git checkout devel
git svn rebase

No error. You might try doing a fresh clone in another directory.

Dan

> How can I update.
> km
> 
> 
> 
> 
> On Tue, Mar 29, 2016 at 4:16 PM, Dan Tenenbaum <dtenenba@fredhutch.org>
> wrote:
> 
> > 
> > 
> > ----- Original Message -----
> > > From: "Karim Mezhoud" <kmezhoud@gmail.com>
> > > To: "bioc-devel" <bioc-devel@r-project.org>
> > > Cc: "Dan Tenenbaum" <dtenenba@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@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

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