From d2e5dec29869b43a90f9acea815ede2ea28bb71d Mon Sep 17 00:00:00 2001
From: Holger Brandl <holgerbrandl@gmail.com>
Date: Tue, 5 Jul 2016 14:48:47 +0200
Subject: [PATCH] finished basic results integration
---
common/cp_enrichment.R | 15 ++++-----------
1 file changed, 4 insertions(+), 11 deletions(-)
diff --git a/common/cp_enrichment.R b/common/cp_enrichment.R
index c6d08dc..d767cb0 100755
--- a/common/cp_enrichment.R
+++ b/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")
--
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