The file ending used for R sources in codeface is .r,
instead of .R for packages.R.
Signed-off-by: Wolfgang Mauerer <wolfgang.mauerer@xxxxxxxxxxxxxxxxx>
---
integration-scripts/install_codeface_R.sh | 3 +-
packages.R | 59 -------------------------------
packages.r | 59 +++++++++++++++++++++++++++++++
3 files changed, 60 insertions(+), 61 deletions(-)
delete mode 100644 packages.R
create mode 100644 packages.r
diff --git a/integration-scripts/install_codeface_R.sh
b/integration-scripts/install_codeface_R.sh
index 05f7c9a..53a9612 100755
--- a/integration-scripts/install_codeface_R.sh
+++ b/integration-scripts/install_codeface_R.sh
@@ -13,5 +13,4 @@ sudo DEBIAN_FRONTEND=noninteractive apt-get -qqy install
r-base r-base-dev r-cra
r-cran-rjson r-cran-lsa r-cran-testthat r-cran-arules r-cran-data.table
\
r-cran-ineq libx11-dev libssh2-1-dev r-bioc-biocinstaller
-sudo Rscript packages.R
-
+sudo Rscript packages.r
diff --git a/packages.R b/packages.R
deleted file mode 100644
index 787e02b..0000000
--- a/packages.R
+++ /dev/null
@@ -1,59 +0,0 @@
-filter.installed.packages <- function(packageList) {
- if("-f" %in% commandArgs(trailingOnly = TRUE)) {
- return(packageList)
- } else {
- return(packageList[which(packageList %in% installed.packages()[,1] ==
FALSE)])
- }
-}
-
-## Remove package from all libraries (i.e., .libPaths())
-remove.installed.packages <- function(pack) {
- for (path in .libPaths()) {
- # try to remove package (hard stop() otherwise, if not existing)
- tryCatch({
- remove.packages(pack, path)
- print(paste("removed previously installed package", pack))
- }, error = function(e) {
- # silently ignore errors (the reason would be that a package
- # is not installed)
- })
- }
-}
-
-## (re-)install a package from github
-reinstall.package.from.github <- function(package, url) {
-
- ## if package is installed, remove it completely from all libraries
- p <- filter.installed.packages(c(package))
- if(length(p) == 0) {
- remove.installed.packages(package)
- }
-
- ## Re-install packages
- devtools::install_github(url)
-}
-
-p <- filter.installed.packages(c("BiRewire", "graph", "Rgraphviz"))
-if(length(p) > 0) {
- source("http://bioconductor.org/biocLite.R";)
- biocLite(p)
-}
-
-p <- filter.installed.packages(c("statnet", "ggplot2", "tm", "optparse",
- "igraph", "zoo", "xts", "lubridate", "xtable",
- "reshape", "wordnet", "stringr", "yaml",
"plyr",
- "scales", "gridExtra", "scales", "RMySQL",
- "RCurl", "mgcv", "shiny", "dtw", "httpuv",
"devtools",
- "corrgram", "logging", "png", "rjson", "lsa",
"RJSONIO"))
-if(length(p) > 0) {
- install.packages(p ,dependencies=T)
-}
-
-
-## Install following packages from different sources
-## and update existing installations, if needed
-reinstall.package.from.github("tm.plugin.mail",
"wolfgangmauerer/tm-plugin-mail/pkg")
-reinstall.package.from.github("snatm", "wolfgangmauerer/snatm/pkg")
-reinstall.package.from.github("shinyGridster", "wch/shiny-gridster")
-reinstall.package.from.github("shinybootstrap2", "rstudio/shinybootstrap2")
-reinstall.package.from.github("Rgraphviz", "mitchell-joblin/Rgraphviz")
diff --git a/packages.r b/packages.r
new file mode 100644
index 0000000..787e02b
--- /dev/null
+++ b/packages.r
@@ -0,0 +1,59 @@
+filter.installed.packages <- function(packageList) {
+ if("-f" %in% commandArgs(trailingOnly = TRUE)) {
+ return(packageList)
+ } else {
+ return(packageList[which(packageList %in% installed.packages()[,1] ==
FALSE)])
+ }
+}
+
+## Remove package from all libraries (i.e., .libPaths())
+remove.installed.packages <- function(pack) {
+ for (path in .libPaths()) {
+ # try to remove package (hard stop() otherwise, if not existing)
+ tryCatch({
+ remove.packages(pack, path)
+ print(paste("removed previously installed package", pack))
+ }, error = function(e) {
+ # silently ignore errors (the reason would be that a package
+ # is not installed)
+ })
+ }
+}
+
+## (re-)install a package from github
+reinstall.package.from.github <- function(package, url) {
+
+ ## if package is installed, remove it completely from all libraries
+ p <- filter.installed.packages(c(package))
+ if(length(p) == 0) {
+ remove.installed.packages(package)
+ }
+
+ ## Re-install packages
+ devtools::install_github(url)
+}
+
+p <- filter.installed.packages(c("BiRewire", "graph", "Rgraphviz"))
+if(length(p) > 0) {
+ source("http://bioconductor.org/biocLite.R";)
+ biocLite(p)
+}
+
+p <- filter.installed.packages(c("statnet", "ggplot2", "tm", "optparse",
+ "igraph", "zoo", "xts", "lubridate", "xtable",
+ "reshape", "wordnet", "stringr", "yaml",
"plyr",
+ "scales", "gridExtra", "scales", "RMySQL",
+ "RCurl", "mgcv", "shiny", "dtw", "httpuv",
"devtools",
+ "corrgram", "logging", "png", "rjson", "lsa",
"RJSONIO"))
+if(length(p) > 0) {
+ install.packages(p ,dependencies=T)
+}
+
+
+## Install following packages from different sources
+## and update existing installations, if needed
+reinstall.package.from.github("tm.plugin.mail",
"wolfgangmauerer/tm-plugin-mail/pkg")
+reinstall.package.from.github("snatm", "wolfgangmauerer/snatm/pkg")
+reinstall.package.from.github("shinyGridster", "wch/shiny-gridster")
+reinstall.package.from.github("shinybootstrap2", "rstudio/shinybootstrap2")
+reinstall.package.from.github("Rgraphviz", "mitchell-joblin/Rgraphviz")
--
2.8.3
