From c0b8b3915f7c17c86f71a58de2e52098a4d703f3 Mon Sep 17 00:00:00 2001 From: vinuesa Date: Sat, 18 Sep 2021 11:05:43 -0500 Subject: [PATCH] install_R_deps.R restored --- install_R_deps.R | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/install_R_deps.R b/install_R_deps.R index ad7be8b..1eef3cd 100755 --- a/install_R_deps.R +++ b/install_R_deps.R @@ -26,7 +26,7 @@ # Instructions to install ape from source, in case it causes kdetrees errors # In MacOS this requires installing gfortran from https://gcc.gnu.org/wiki/GFortranBinaries # $ R -# > install.packages("ape",dependencies=TRUE, lib="lib/R", type="source") +# > install.packages("ape", dependencies=TRUE, lib="lib/R", type="source") # > install.packages("kdetrees",dependencies=TRUE, lib="lib/R", type="source") repository = 'https://cloud.r-project.org'; #'http://cran.rstudio.com' @@ -34,7 +34,7 @@ repository = 'https://cloud.r-project.org'; #'http://cran.rstudio.com' # do not change (reduce), as it includes dependencies for the GET_HOM+GET_PHYLO image, # and from v2.3.0 (2021-09-18) the GET_PHYLO package also includes hcluster_pangenome_matrix.sh, which require "cluster", "dendextend", "factoextra" # ape and kdetrees are installed from source -required_packages = c("stringr", "vioplot", "ggplot2", "gplots", "dplyr", "seqinr", "plyr", "cluster", "dendextend", "factoextra", "Rcpp") +required_packages = c("ape", "kdetrees", "stringr", "vioplot", "ggplot2", "gplots", "dplyr", "seqinr", "plyr", "cluster", "dendextend", "factoextra") local_lib = "./lib/R" @@ -44,7 +44,7 @@ local_lib = "./lib/R" #remove.packages(c("ape", "cluster", "dendextend", "factoextra", "kdetrees"), lib=local_lib) # Install ape && kdetrees from source -install.packages(c("ape", "kdetrees"), dependencies=TRUE, lib="lib/R", type="source") +# install.packages(c("ape", "kdetrees"), dependencies=TRUE, lib="lib/R", type="source") # install the remaining required R packages for (package in required_packages) { @@ -54,5 +54,4 @@ for (package in required_packages) { } } - sessionInfo()