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Where to put package vignettes

8 messages · Guillermo.Vinue at uv.es, Søren Højsgaard, Baptiste Auguie +2 more

Original
Guillermo.Vinue at uv.es
# 
Dear R-devel list,

My name is Guillermo Vinu?. I have created an R package that includes a
vignette. Earlier on, to test my package, I tried to install it both in
Linux and Windows and it worked. My vignette was in /inst/doc.

Now, I have finished for good and before submitting my package to CRAN
I've tried to install it again first in Linux and then in Windows (I
removed that first installation some time ago).

My package was succesfully installed in Linux (Fedora 18 and R 2.15.2)
and the vignette was available. However, when trying to install it in
Windows (R 3.0.2), unfortunately the vignette didn't appear. My vignette
is build with knitr. 

In fact, if I first install the package on Windows, the vignette is
accesible, but then in Linux, not.

I have read that as from R 2.14.0 the preferred location for the Sweave
sources is the subdirectory vignettes of the source packages, but for
compatibility with earlier versions of R, vignette sources will be
looked for in inst/doc if vignettes does not exist.

Where do I have to put my vignette so that it could be available with
any installation and which files (.Rnw or .pdf) should be included?. 

I hope you can clarify my doubts. I have seen the collection of prior
postings to the list, but I have not found a specifical answer to my doubts .

Thank you very much in advance.

Best regards,

Guillermo
Søren Højsgaard
# 
My understanding is this:

1) Put vignettes files (.Rnw files) in the /vignettes subdirectory. 2) Build the package foo with R CMD build foo. 3) Install the package with R CMD INSTALL foo_xxx.tar.gz

Then the vignettes will be available. However you can also install the package with R CMD INSTALL foo, but then the vignettes will *not* be available (because it is in the build process that the vignettes go from /vignettes to /inst/doc)

Regards 
S?ren


-----Original Message-----
From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-project.org] On Behalf Of Guillermo.Vinue at uv.es
Sent: 20. februar 2014 12:19
To: r-devel at r-project.org
Subject: [Rd] Where to put package vignettes

Dear R-devel list,

My name is Guillermo Vinu?. I have created an R package that includes a vignette. Earlier on, to test my package, I tried to install it both in Linux and Windows and it worked. My vignette was in /inst/doc.

Now, I have finished for good and before submitting my package to CRAN I've tried to install it again first in Linux and then in Windows (I removed that first installation some time ago).

My package was succesfully installed in Linux (Fedora 18 and R 2.15.2) and the vignette was available. However, when trying to install it in Windows (R 3.0.2), unfortunately the vignette didn't appear. My vignette is build with knitr. 

In fact, if I first install the package on Windows, the vignette is accesible, but then in Linux, not.

I have read that as from R 2.14.0 the preferred location for the Sweave sources is the subdirectory vignettes of the source packages, but for compatibility with earlier versions of R, vignette sources will be looked for in inst/doc if vignettes does not exist.

Where do I have to put my vignette so that it could be available with any installation and which files (.Rnw or .pdf) should be included?. 

I hope you can clarify my doubts. I have seen the collection of prior postings to the list, but I have not found a specifical answer to my doubts .

Thank you very much in advance.

Best regards,

Guillermo

______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Guillermo.Vinue at uv.es
# 
Dear S?ren,

Thank you very much for your answer, it solved my problem and now my
package can be installed both on Linux and Windows and the vignette is
available in both systems. I put the vignette in /vignettes.

However, unfortunately my problems have not ended here. As mentioned, my
vignette is built with knitr and with the following commands:

1) R CMD check foo
2) R CMD build foo
3) R CMD INSTALL foo_xxx.tar.gz

the vignette is built with Sweave!

I have read in http://yihui.name/knitr/demo/vignette/ that in that case,
a Makefile should be incorporated.

I have incorporated in /inst/doc the makefile from
https://github.com/yihui/knitr/blob/7eb34104/inst/doc/Makefile

however, my vignette is still built with Sweave. I use R 2.15.2.

How can I fix this performance?.

Thank you very much again.

Best regards,

Guillermo
Build the package foo with R CMD build foo. 3) Install the package with
R CMD INSTALL foo_xxx.tar.gz
package with R CMD INSTALL foo, but then the vignettes will *not* be
available (because it is in the build process that the vignettes go from
/vignettes to /inst/doc)
[mailto:r-devel-bounces at r-project.org] On Behalf Of Guillermo.Vinue at uv.es
a vignette. Earlier on, to test my package, I tried to install it both
in Linux and Windows and it worked. My vignette was in /inst/doc.
I've tried to install it again first in Linux and then in Windows (I
removed that first installation some time ago).
and the vignette was available. However, when trying to install it in
Windows (R 3.0.2), unfortunately the vignette didn't appear. My vignette
is build with knitr.
accesible, but then in Linux, not.
Sweave sources is the subdirectory vignettes of the source packages, but
for compatibility with earlier versions of R, vignette sources will be
looked for in inst/doc if vignettes does not exist.
any installation and which files (.Rnw or .pdf) should be included?.
postings to the list, but I have not found a specifical answer to my
doubts .
Søren Højsgaard
# 
Guillermino,

Sorry but I've never made it beyond Sweave in connection with R packages; we will have to wait for more insight from others.

S?ren

-----Original Message-----
From: Guillermo.Vinue at uv.es [mailto:Guillermo.Vinue at uv.es] 
Sent: 20. februar 2014 15:43
To: S?ren H?jsgaard
Cc: r-devel at r-project.org
Subject: RE: [Rd] Where to put package vignettes

Dear S?ren,

Thank you very much for your answer, it solved my problem and now my package can be installed both on Linux and Windows and the vignette is available in both systems. I put the vignette in /vignettes.

However, unfortunately my problems have not ended here. As mentioned, my vignette is built with knitr and with the following commands:

1) R CMD check foo
2) R CMD build foo
3) R CMD INSTALL foo_xxx.tar.gz

the vignette is built with Sweave!

I have read in http://yihui.name/knitr/demo/vignette/ that in that case, a Makefile should be incorporated.

I have incorporated in /inst/doc the makefile from https://github.com/yihui/knitr/blob/7eb34104/inst/doc/Makefile

however, my vignette is still built with Sweave. I use R 2.15.2.

How can I fix this performance?.

Thank you very much again.

Best regards,

Guillermo
Build the package foo with R CMD build foo. 3) Install the package with R CMD INSTALL foo_xxx.tar.gz
package with R CMD INSTALL foo, but then the vignettes will *not* be available (because it is in the build process that the vignettes go from /vignettes to /inst/doc)
[mailto:r-devel-bounces at r-project.org] On Behalf Of Guillermo.Vinue at uv.es
a vignette. Earlier on, to test my package, I tried to install it both in Linux and Windows and it worked. My vignette was in /inst/doc.
I've tried to install it again first in Linux and then in Windows (I removed that first installation some time ago).
and the vignette was available. However, when trying to install it in Windows (R 3.0.2), unfortunately the vignette didn't appear. My vignette is build with knitr.
accesible, but then in Linux, not.
Sweave sources is the subdirectory vignettes of the source packages, but for compatibility with earlier versions of R, vignette sources will be looked for in inst/doc if vignettes does not exist.
any installation and which files (.Rnw or .pdf) should be included?.
postings to the list, but I have not found a specifical answer to my doubts .
Hadley Wickham
# 
You also need to make sure that your knitr vignettes include

%\VignetteEngine{knitr::knitr}

See http://yihui.name/knitr/demo/vignette/ for full details.

Hadley

On Thu, Feb 20, 2014 at 8:56 AM, baptiste auguie
<baptiste.auguie at gmail.com> wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Yihui Xie
    

    

      
      #
    

  


  

      
It is not guaranteed that knitr vignettes will work for R < 3.0.x
(even with the Makefile approach, which was really a hack). Unless you
must stay with R 2.15.x, you are strongly recommended to upgrade to R
3.0.x and forget about the Makefile approach. Then follow the three
steps mentioned in http://yihui.name/knitr/demo/vignette/

If you still cannot work it out, please point us to the source of your package.

Regards,
Yihui
--
Yihui Xie <xieyihui at gmail.com>
Web: http://yihui.name

        
On Thu, Feb 20, 2014 at 8:43 AM,  <Guillermo.Vinue at uv.es> wrote:

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Guillermo.Vinue at uv.es
    

    

      
      #
    

  


  

      
Dear All,

As you mentioned, it was a matter of upgrading R. Now I have R 3.0.2 and
everything has worked well.

Thank you very much for all your comments and suggestions. They have
been very helpful.

Best regards,

Guillermo

            

      
      
      
    

        
package.

            

      
      
      
    

        
Guillermo.Vinue at uv.es