[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: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "bioc-devel" <bioc-devel at 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 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