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

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").

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
S?ren

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

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").

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
S?ren

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

Sorry, yes it is plural - but changing to plural has no effect.

Regards
S?ren

-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
Sent: 30. juni 2013 23:09
To: S?ren H?jsgaard
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, S?ren H?jsgaard 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
S?ren

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

--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

vignette(package="gRbase")

Sorry, yes it is plural - but changing to plural has no effect.

Regards
S?ren

-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
Sent: 30. juni 2013 23:09
To: S?ren H?jsgaard
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, S?ren H?jsgaard 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
S?ren

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

--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

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.