[Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!
dtenenba at fredhutch.org
Tue Mar 29 17:12:33 CEST 2016
----- 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:
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 (
> I am following scenario 2.
> When I fork bioc-mirror/canceR I get two repo with the same name in my
> 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
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
You cannot, the repositories in bioc-mirror are read-only.
> Thank you
> On Wed, Mar 23, 2016 at 10:44 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
>> 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
>> 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:
>> For non-sweave (usually knitr) vignettes, the important things to check
>> - 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
>> 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
>> If you've tried all these things and are still running into problems,
>> contact bioc-devel.
>> Bioc-devel at r-project.org mailing list
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