finished basic results integration

common/cp_enrichment.R

@@ -20,9 +20,9 @@ Options:
 opts <- docopt(doc, commandArgs(TRUE)) ## does not work when spining
 # opts <- docopt(doc, "--overlay_expr_data ../plot_score_matrix.txt ../degs_by_contrast.txt contrast" )
 
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.26/R/core_commons.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.26/R/ggplot_commons.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.26/R/bio/diffex_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.27/R/core_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.27/R/ggplot_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.27/R/bio/diffex_commons.R")
 
 loadpack(knitr)
 loadpack(DT)
@@ -427,14 +427,7 @@ dir.create(pwPlotDir)
 # session::restore.session(".pview_debug.dat");
 
 ## from http://stackoverflow.com/questions/7505547/detach-all-packages-while-working-in-r
-## todo remove this once we use v1.27 of core_commons
-detachAllPackages <- function() {
-    basic.packages <- c("package:stats","package:graphics","package:grDevices","package:utils","package:datasets","package:methods","package:base")
-    package.list <- search()[ifelse(unlist(gregexpr("package:",search()))==1,TRUE,FALSE)]
-    package.list <- setdiff(package.list,basic.packages)
-    if (length(package.list)>0)  for (package in package.list) detach(package, character.only=TRUE)
-}
-detachAllPackages()
+unload_packages()
 
 
 devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.26/R/core_commons.R")