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

[Karim Mezhoud]

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 <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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