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authorChristoph Helma <helma@in-silico.ch>2016-03-24 13:43:27 +0100
committerChristoph Helma <helma@in-silico.ch>2016-03-24 13:43:27 +0100
commit90fbe8b3ef3fa05aa308e6650e11d690bb89b200 (patch)
tree524a984f6108188da15f9a25ad31ec314a294f89 /lib/lazar.rb
parent130524b0efa98f6e63d39c55e2f643130459ceee (diff)
local R package installation
Diffstat (limited to 'lib/lazar.rb')
-rw-r--r--lib/lazar.rb18
1 files changed, 6 insertions, 12 deletions
diff --git a/lib/lazar.rb b/lib/lazar.rb
index b4293e9..22dfd2b 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -40,17 +40,18 @@ when "development"
end
# R setup
+rlib = File.expand_path(File.join(File.dirname(__FILE__),"..","R"))
# should work on POSIX including os x
# http://stackoverflow.com/questions/19619582/number-of-processors-cores-in-command-line
NR_CORES = `getconf _NPROCESSORS_ONLN`.to_i
R = Rserve::Connection.new
R.eval "
suppressPackageStartupMessages({
- library(ggplot2)
- library(grid)
- library(gridExtra)
- library(caret)
- library(doMC)
+ library(ggplot2,lib=\"#{rlib}\")
+ library(grid,lib=\"#{rlib}\")
+ library(gridExtra,lib=\"#{rlib}\")
+ library(caret,lib=\"#{rlib}\")
+ library(doMC,lib=\"#{rlib}\")
registerDoMC(#{NR_CORES})
})
"
@@ -58,13 +59,6 @@ suppressPackageStartupMessages({
# Require sub-Repositories
require_relative '../openbabel/lib/openbabel'
-# Fminer environment variables
-ENV['FMINER_SMARTS'] = 'true'
-ENV['FMINER_NO_AROMATIC'] = 'true'
-ENV['FMINER_PVALUES'] = 'true'
-ENV['FMINER_SILENT'] = 'true'
-ENV['FMINER_NR_HITS'] = 'true'
-
# OpenTox classes and includes
CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules