Hi,

For me, three solutions :
 - You can find existing packages which will install your library (https://testtoolshed.g2.bx.psu.edu/view/jeltje/package_dnacopy_1_40_0/118417199f06). So you will just need to link a requirement (https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Crequirements.3E_tag_set) and a tool_dependencies.xml file
 - If not, you can write your own package. But thanks to Ross Lazarus, to deal with dependencies of dependencies of dependencies, there is a tool for that https://testtoolshed.g2.bx.psu.edu/view/fubar/biocdepgen_r_3_1_2/faafc60f3d6a
 - If you lack of time, you install R and needed libraries on your serveur.

Unfortunately, I can’t explain you why you couldn’t install your library through your script because R use to allow installing in the user home.


Gildas

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Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
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Le 26 févr. 2016 à 09:03, Xianrong Wong <wongxr@gmail.com> a écrit :

Hi,
    I am trying to package an R script (that requires certain R packages) into a galaxy tool.  Any advice would be deeply appreciated!  

I have tested it on planemo and it works.  When I tried the version I uploaded onto the toolshed, I got an error saying that the R packages do not exist.  I next added the following lines to the R script:

source("https://bioconductor.org/biocLite.R")

biocLite()

biocLite(c("DNAcopy", "preprocessCore"))

and I got the following error when running the installed tool on galaxy:


Installing package(s) ‘DNAcopy’, ‘preprocessCore’
Warning in install.packages(pkgs = doing, lib = lib, ...) :
  'lib = "/usr/local/lib/R/site-library"' is not writable
Error in install.packages(pkgs = doing, lib = lib, ...) : 
  unable to install packages
Calls: biocLite ... .biocLiteInstall -> .reposInstall -> install.packages
Execution halted
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