BwUniCluster2.0/Software/R/stringi

Note that the instructions provided below refer to R 4.2.1 (but not R 4.3.3)! We are currently updating our guides for R 4.3.3.

General information

stringi is an R package for fast, portable, correct, consistent, and convenient string/text processing in any locale or character encoding.

Installation

Please enter the following code, presented in the boxes below, directly in your shell/command line on bwUniCluster

Preparations

Prepare .R directory (if it does not already exists). This is then filled with information how R should compile the packages ('compiler flags'). These are written (and can be reviewed) into the (text) file Makevars.

If you already have a .R/Makevars file, check whether these flags are already set.

cat ~/.R/Makevars

In this case, skip the following block of five commands. If this is not the case, enter the following commands in your shell (command line).

mkdir -p ~/.R
echo "CXX14=icpc" >> ~/.R/Makevars
echo "CXX17=icpc" >> ~/.R/Makevars
echo "CXX14FLAGS=-O3 -fPIC -std=c++14 -wd308 -axCORE-AVX512,CORE-AVX2,AVX -xSSE4.2 -fp-model strict -qopenmp" >> ~/.R/Makevars
echo "CXX17FLAGS=-O3 -fPIC -std=c++17 -wd308 -axCORE-AVX512,CORE-AVX2,AVX -xSSE4.2 -fp-model strict -qopenmp" >> ~/.R/Makevars
echo "CXXFLAGS += -wd308" >> ~/.R/Makevars
echo "PKG_CXXFLAGS += -std=c++14 -wd308" >> ~/.R/Makevars

The installation of stringi makes use other libraries (C/C++ and Java libraries for Unicode and globalization, icu4c Intel) which need to be loaded before installation (and R, of course).

module purge 	
module load math/R
module load lib/icu4c/74.1_intel2021.4.0

Installing the R package

We can now install stringi (in its development version) and its dependencies within a R session

R -q
> install.packages("stringi")

Testing the installation

To check whether the installation worked, make a test run in R

> library(stringi)
> stri_length(c("Hello", "world", "!"))
[1] 5 5 1

Note that you always need to load

module load math/R/4.1.2
module load lib/icu4c/74.1_intel2021.4.0

to your batch job scripts that use stringi or to run them directly in the command line if you use an interactive session.