## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
## ----eval=FALSE---------------------------------------------------------------
# if (!require("devtools")) install.packages("devtools") # to install
# install.packages("tidyverse")
## ----eval=FALSE---------------------------------------------------------------
# install.packages("gsl")
## ----eval=FALSE---------------------------------------------------------------
# devtools::install_github("thierrygosselin/grur")
# devtools::install_github("thierrygosselin/assigner")
## ----eval=FALSE---------------------------------------------------------------
# usethis::edit_r_makevars()
## ----eval=FALSE---------------------------------------------------------------
# #Warning: cannot remove prior installation of package ‘stringi’
## ----eval=FALSE---------------------------------------------------------------
# file.exists("~/.Renviron")
## ----eval=FALSE---------------------------------------------------------------
# Sys.getenv("LD_LIBRARY_PATH")
# # [1]""
## ----eval=FALSE---------------------------------------------------------------
# # in R:
# Sys.setenv(LD_LIBRARY_PATH="/usr/local/lib/")
# # For Linux you could use: /usr/local/lib/:/usr/lib64
## ----eval=FALSE---------------------------------------------------------------
# Sys.setenv(LD_LIBRARY_PATH="/usr/local/lib64/R/lib:/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.amzn2.0.1.x86_64/jre/lib/amd64/server:/usr/local/lib/:/usr/lib64")
## ----eval=FALSE---------------------------------------------------------------
# install.packages("rgeos", repos="http://R-Forge.R-project.org", type="source")
# install.packages("rgdal", repos="http://R-Forge.R-project.org", type="source")
# devtools::install_github("r-spatial/sf", configure.args = "--with-proj-lib=/usr/local")
# install.packages("adegenet")
## ----eval=FALSE---------------------------------------------------------------
# BiocManager::install("SeqArray")
## ----eval=FALSE---------------------------------------------------------------
# remotes::install_local(path = "SeqArray_latest.tar.gz")
## ----eval=FALSE---------------------------------------------------------------
# Error: C stack usage 7971092 is too close to the limit
## ----eval=FALSE---------------------------------------------------------------
# usethis::edit_r_makevars()
## ----eval=FALSE---------------------------------------------------------------
# #fstcore fst data.table
# CC=/usr/local/bin/gcc -fopenmp
# CXX=/usr/local/bin/g++ -fopenmp
# CXX11=/usr/local/bin/g++ -fopenmp
# CXX14=/usr/local/bin/g++ -fopenmp
# CXX17=/usr/local/bin/g++ -fopenmp
# CXX1X=/usr/local/bin/g++ -fopenmp
# CXX98=/usr/local/bin/g++ -fopenmp
## ----eval=FALSE---------------------------------------------------------------
# install.packages("fstcore", type = "source")
# install.packages("fst", type = "source")
# install.packages("data.table", type = "source")
## ----eval=FALSE---------------------------------------------------------------
# usethis::edit_r_makevars()
## ----eval=FALSE---------------------------------------------------------------
# usethis::edit_r_makevars()
## ----eval=FALSE---------------------------------------------------------------
# require(xgboost)
# x <- matrix(rnorm(100*10000), 10000, 100)
# y <- x %*% rnorm(100) + rnorm(1000)
#
# system.time({bst = xgboost(data = x, label = y, nthread = 1, nround = 100, verbose = FALSE)})
# system.time({bst = xgboost(data = x, label = y, nthread = 4, nround = 100, verbose = FALSE)})
## ----eval=FALSE---------------------------------------------------------------
# usethis::edit_r_makevars()
## ----eval=FALSE---------------------------------------------------------------
# install.packages("ranger")
## ----eval=FALSE---------------------------------------------------------------
# install.packages("missRanger")
## ----eval=FALSE---------------------------------------------------------------
# install.packages("miceRanger")
## ----eval=FALSE---------------------------------------------------------------
# BiocManager::install("pcaMethods")
## ----terminal_folder_shortcut.png, echo=FALSE---------------------------------
knitr::include_graphics("terminal_folder_shortcut.png")
## ----copy_path.png, echo=FALSE------------------------------------------------
knitr::include_graphics("copy_path.png")
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