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

[Dan Tenenbaum]

----- 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.

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 <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
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