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 <lig...@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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