R help - Nov 2011 - cannot set the path to installed R packages when building a package vignette

Dear colleagues,

I am having issues trying to build a R package I recently wrote.
I am using R 2.14.0 and my package depends on another package called aod.
Running:
R CMD Sweave vignette.Rnw
is perfectly fine and the vignette compiles properly.

but when I use
R CMD build mypackage
to build the tar.gz  I get the following error:

 * installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: aod
Warning in library(pkg, character.only = TRUE, logical.return = TRUE,
lib.loc = lib.loc) :
  there is no package called ‘aod’

Error: processing vignette ‘ExomeDepth-vignette.Rnw’ failed with
diagnostics:
 chunk 1 (label = load)
Error : package ‘aod’ could not be loaded
Execution halted

I can fix the issue by inserting the following line into my vignette:
.libPaths(c("/ugi/home/shared/vincent/libraries/R/installed",
.libPaths()))
where the path specifies the installation path to my R packages. But
clearly this should not be part of the vignette.

Basically I cannot find a good way to specify a path to my installed
packages when I run
R CMD build
I cannot find the right info. I am probably being slow but if someone could
point me to the right direction, any help would be very much appreciated.

Thank you in advance,

Vincent






-- 
Vincent Plagnol
University College London Genetics Institute
Darwin building, office 210
Gower Street, London, WC1E 6BT
Cell: +44-(0)7946-546923
Office: +44-(0) 2031-084002
Website: http://www.ucl.ac.uk/ugi/research/VincentPlagnol
ResearcherID: http://www.researcherid.com/rid/A-5667-2011

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On 19.11.2011 00:14, Vincent Plagnol wrote:
> Dear colleagues,
>
> I am having issues trying to build a R package I recently wrote.
> I am using R 2.14.0 and my package depends on another package called aod.
> Running:
> R CMD Sweave vignette.Rnw
> is perfectly fine and the vignette compiles properly.
>
> but when I use
> R CMD build mypackage
> to build the tar.gz  I get the following error:
>
>   * installing the package to re-build vignettes
> * creating vignettes ... ERROR
> Loading required package: aod
> Warning in library(pkg, character.only = TRUE, logical.return = TRUE,
> lib.loc = lib.loc) :
>    there is no package called ?aod?
>
> Error: processing vignette ?ExomeDepth-vignette.Rnw? failed with
> diagnostics:
>   chunk 1 (label = load)
> Error : package ?aod? could not be loaded
> Execution halted
>
> I can fix the issue by inserting the following line into my vignette:
> .libPaths(c("/ugi/home/shared/vincent/libraries/R/installed",
.libPaths()))
> where the path specifies the installation path to my R packages. But
> clearly this should not be part of the vignette.
>
> Basically I cannot find a good way to specify a path to my installed
> packages when I run
> R CMD build
> I cannot find the right info. I am probably being slow but if someone could
> point me to the right direction, any help would be very much appreciated.

If the packages are not on your default search path, set the environment 
variable R_LIBS appropriately before running R CMD build.

Best,
Uwe Ligges

> Thank you in advance,
>
> Vincent
>
>
>
>
>
>
>
>
>
> ______________________________________________
> 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.

Uwe,

thanks it worked just fine.
I think I was confused by the fact that .Rprofile sets the library path
properly when I use R interactively or it BATCH mode but I need to set my
R_LIBS (in .Renviron worked for me) when I use "R CMD build".

In any case it fixes my problem so many thanks again,

Vincent





On Sat, Nov 19, 2011 at 6:14 PM, Uwe Ligges
<ligges@statistik.tu-dortmund.de
> wrote:
>
>
> On 19.11.2011 00:14, Vincent Plagnol wrote:
> > Dear colleagues,
> >
> > I am having issues trying to build a R package I recently wrote.
> > I am using R 2.14.0 and my package depends on another package called
aod.
> > Running:
> > R CMD Sweave vignette.Rnw
> > is perfectly fine and the vignette compiles properly.
> >
> > but when I use
> > R CMD build mypackage
> > to build the tar.gz  I get the following error:
> >
> >   * installing the package to re-build vignettes
> > * creating vignettes ... ERROR
> > Loading required package: aod
> > Warning in library(pkg, character.only = TRUE, logical.return = TRUE,
> > lib.loc = lib.loc) :
> >    there is no package called ‘aod’
> >
> > Error: processing vignette ‘ExomeDepth-vignette.Rnw’ failed with
> > diagnostics:
> >   chunk 1 (label = load)
> > Error : package ‘aod’ could not be loaded
> > Execution halted
> >
> > I can fix the issue by inserting the following line into my vignette:
> >
.libPaths(c("/ugi/home/shared/vincent/libraries/R/installed",
> .libPaths()))
> > where the path specifies the installation path to my R packages. But
> > clearly this should not be part of the vignette.
> >
> > Basically I cannot find a good way to specify a path to my installed
> > packages when I run
> > R CMD build
> > I cannot find the right info. I am probably being slow but if someone
> could
> > point me to the right direction, any help would be very much
appreciated.
>
>
> If the packages are not on your default search path, set the environment
> variable R_LIBS appropriately before running R CMD build.
>
> Best,
> Uwe Ligges
>
>
> > Thank you in advance,
> >
> > Vincent
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > ______________________________________________
> > R-help@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.
>
>
>

-- 
Vincent Plagnol
University College London Genetics Institute
Darwin building, office 210
Gower Street, London, WC1E 6BT
Cell: +44-(0)7946-546923
Office: +44-(0) 2031-084002
Website: http://www.ucl.ac.uk/ugi/research/VincentPlagnol
ResearcherID: http://www.researcherid.com/rid/A-5667-2011

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