[R] Vignettes do not appear on CRAN if files are placed in /vignette subdirectory - but they do appear if placed in /inst/doc

[Søren Højsgaard]

gRbase use graph, RBGL and Rgraphviz from bioconductor. My understanding is that if I put vignettes into /vignettes then R CMD build will build the vignettes and put them into /inst/doc and this works:

gRbase/inst/
gRbase/inst/CITATION
gRbase/inst/doc/
gRbase/inst/doc/gRbase-arrayops1.R
gRbase/inst/doc/gRbase-arrayops1.Rnw
gRbase/inst/doc/gRbase-arrayops1.pdf
gRbase/inst/doc/gRbase-arrayops2.R
gRbase/inst/doc/gRbase-arrayops2.Rnw
gRbase/inst/doc/gRbase-arrayops2.pdf
gRbase/inst/doc/gRbase-graphs.R
gRbase/inst/doc/gRbase-graphs.Rnw
gRbase/inst/doc/gRbase-graphs.pdf

After installing I then get
> vignette(package="gRbase")
no vignettes found

sorenh at sorenh:~/docs/stat/Rdevel/gmwR-DEVEL/gRbaseDEVEL$ R --version
R version 3.0.1 (2013-05-16) -- "Good Sport"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

However, Martin Morgan reports that it works for him. I don't know what to make of this. 

Regards
Søren




-----Original Message-----
From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com] 
Sent: 1. juli 2013 00:45
To: Søren Højsgaard
Cc: Martin Morgan; R hELP (r-help at stat.math.ethz.ch)
Subject: Re: [R] Vignettes do not appear on CRAN if files are placed in /vignette subdirectory - but they do appear if placed in /inst/doc

On 13-06-30 5:28 PM, Søren Højsgaard wrote:
> Sorry, yes it is plural - but changing to plural has no effect.

CRAN has had some problems building vignettes in cases where the vignette depends on packages that are not installed on CRAN.  Could that be the problem?  (They are working on fixing this.)

My tables package has a vignette in the vignettes directory, and it shows up on CRAN, so if it is not the above, there may be other problems.

I am currently involved in redoing the build/INSTALL code for vignettes (which is currently somewhat inconsistent), but I don't know when the new code will be ready.

Duncan Murdoch

> Regards
> Søren
>
> -----Original Message-----
> From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
> Sent: 30. juni 2013 23:09
> To: Søren Højsgaard
> Cc: R hELP (r-help at stat.math.ethz.ch)
> Subject: Re: [R] Vignettes do not appear on CRAN if files are placed 
> in /vignette subdirectory - but they do appear if placed in /inst/doc
>
> On 06/30/2013 01:31 PM, Søren Højsgaard wrote:
>> Dear all,
>>
>> In my gRbase package there are 3 vignettes placed in the /vignette subdirectory. These vignettes do not appear on http://cran.r-project.org/web/packages/gRbase/index.html and neither do they appear if I open a browser with help("gRbase").
>>
>
>
> the directory name is plural -- vignettes.
>
> Martin
>
>> However, if instead I place the vignettes in /inst/doc then they will appear in the browser opened with help("gRbase") - and they also appear on CRAN.
>>
>> Is this how it should be or am I missing something?
>>
>> Best regards
>> Søren
>>
>>
>>
>>> sessionInfo()
>> R version 3.0.1 Patched (2013-06-11 r62941)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=Danish_Denmark.1252  LC_CTYPE=Danish_Denmark.1252 [3]
>> LC_MONETARY=Danish_Denmark.1252 LC_NUMERIC=C [5]
>> LC_TIME=Danish_Denmark.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>>    [1] gRain_1.1-2             gRbase_1.6-10           graph_1.38.0
>>    [4] igraph_0.6.5-2          RcppArmadillo_0.3.900.0 RcppEigen_0.3.1.2.1
>>    [7] Matrix_1.0-12           lattice_0.20-15         Rcpp_0.10.3
>> [10] MASS_7.3-26             shTools_1.0             markdown_0.5.4
>> [13] knitr_1.2
>>
>> loaded via a namespace (and not attached):
>>    [1] BiocGenerics_0.6.0 digest_0.6.3       evaluate_0.4.3     formatR_0.7
>>    [5] grid_3.0.1         parallel_3.0.1     RBGL_1.36.2        stats4_3.0.1
>>    [9] stringr_0.6.2      tools_3.0.1
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
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