fixes PecanProject#1073 and tests that packages listed in check.all.s…

…h match packages in all/data/pecan.packages.csv

.bzrignore

@@ -37,3 +37,4 @@ running
 .project
 .settings
 .buildpath
+all/inst/tests/$HOME

all/data/pecan.packages.csv

@@ -1,3 +1,4 @@
-1;2;3;4;5;6;7;8;9;10;11;12
-"utils";"common";"db";"modules/meta.analysis";"modules/uncertainty";"modules/emulator";"modules/assim.batch";"modules/assim.sequential";"modules/data.land";"models/c4photo";"models/ed";"models/sipnet";"all"
+1;2;3;4;5;6;7;8;9;10;11;12;13;14
+"utils";"common";"db";"modules/meta.analysis";"modules/uncertainty";"modules/emulator";"modules/assim.batch";"modules/assim.sequential";"modules/data.land";"modules/rtm";"models/c4photo";"models/ed";"models/sipnet";"all"
+
 

db/inst/tests/derive.traits.R → db/inst/tests/test.derive.traits.R

@@ -6,15 +6,15 @@
 # which accompanies this distribution, and is available at
 # http://opensource.ncsa.illinois.edu/license.html
 #-------------------------------------------------------------------------------
-test_that("take.samples works";{
+test_that("take.samples works",{
   expect_equal(take.samples(summary = data.frame(mean = 1, stat = NA)), 1)
   set.seed(0)
   test.sample <- take.samples(summary = data.frame(mean = 1, stat = 1),
                                sample.size = 2)
   expect_equal(test.sample, c(2.26295428488079, 0.673766639294351))
 })
 
-test_that("derive.trait works";{
+test_that("derive.traits works",{
   set.seed(0)
   input <- list(x = data.frame(mean = 1, stat = 1, n = 1))
   test.derived <- derive.trait(FUN = function(x){1/x},

models/c4photo/NAMESPACE

@@ -1,3 +1,2 @@
-export(remove.config.SIPNET)
+export(remove.config.c4photo)
 export(write.config.c4photo)
-import(PEcAn.utils)

models/c4photo/R/write.configs.c4photo.R

@@ -69,33 +69,6 @@ write.config.c4photo <- function(defaults = NULL,
 }
 #==================================================================================================#
 
-
-#--------------------------------------------------------------------------------------------------#
-##'
-##' @name write.run.generic
-##' @title Function to generate generic model run script files
-##' @author
-##' @import PEcAn.utils
-#--------------------------------------------------------------------------------------------------#
-write.run.generic <- function(settings){
-  run.script.template = system.file("data", "run.template.generic", package="PEcAn.generic")
-  run.text <- scan(file = run.script.template, 
-                   what="character",sep='@', quote=NULL, quiet=TRUE)
-  run.text  <- gsub('TMP', paste("/scratch/",Sys.getenv("USER"),sep=""), run.text)
-  run.text  <- gsub('BINARY', settings$run$host$ed$binary, run.text)
-  run.text <- gsub('OUTDIR', settings$run$host$outdir, run.text)
-  runfile <- paste(settings$outdir, 'run', sep='')
-  writeLines(run.text, con = runfile)
-  if(settings$run$host$name == 'localhost') {
-    system(paste('cp ', runfile, settings$run$host$rundir))
-  }else{
-    system(paste("rsync -outi ", runfile , ' ', settings$run$host$name, ":",
-                 settings$run$host$rundir, sep = ''))
-  }
-}
-#==================================================================================================#
-
-
 #--------------------------------------------------------------------------------------------------#
 ##'
 ##' Clear out previous config and parameter files.

scripts/check.all.sh

@@ -1,4 +1,4 @@
-for f in common utils db modules/meta.analysis modules/uncertainty modules/rtm models/ed
+for f in utils common db modules/meta.analysis modules/uncertainty modules/emulator modules/assim.batch modules/assim.sequential modules/data.land modules/rtm models/c4photo models/ed models/sipnet all
 #-------------------------------------------------------------------------------
 # Copyright (c) 2012 University of Illinois, NCSA.
 # All rights reserved. This program and the accompanying materials