In RubD/Giotto_site: Spatial Single-Cell Transcriptomics Toolbox

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1. First time R package installation

Package development prerequisites

If this is the first time you build and install an R package you can follow this link, which has simple installation instructions for Windows, Mac OSX and Linux.

To specifically install the command-line tools of Xcode for Mac OSX you might also need to run this line in terminal:

xcode-select --install

\

2. Clang error on MacOS

If you see this error on your MacOS:

clang: error: unsupported option ‘-fopenmp’

You can install another clang and point R to use that clang, which supports the -fopenmp paramter. This solution was provided on stackoverflow

1. Install llvm on your mac

brew install llvm

1. create a Makevars file

touch ~/.R/Makevars

1. Add these lines to the Makevars file ```{bash, eval = FALSE}

comment out first line 'CC= ... if there are errors with compiling a package

CC=/usr/local/opt/llvm/bin/clang -fopenmp CXX=/usr/local/opt/llvm/bin/clang++

Also potentially CXX11 (for C++11 compiler)

CXX11=/usr/local/opt/llvm/bin/clang++

-O3 should be faster than -O2 (default) level optimisation ..

CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe LDFLAGS=-L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib CPPFLAGS=-I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include ```

RubD/Giotto_site documentation built on April 12, 2025, 6:46 p.m.