0. 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


1. Python manual installation

Install with pip in python 3

For OSX, Windows or Linux:

pip3 install pandas python-igraph networkx python-louvain leidenalg scikit-learn smfishHmrf

Conda install

If pip install does not work, try installing them within a conda conda environment. Something like this might work, see also this link

1. create yaml file (e.g. environment.yml) with the following information:
name: giotto_env
 — defaults
 — pip=3.4
 — pandas
 — networkx
 - python-igraph
 - leidenalg
 - python-louvain
 - python.app (!!only for OSX!!)
 - scikit-learn
prefix: /Users/your_username/anaconda3/envs/giotto_env
2. create conda environment based on yaml file:
conda env create -f environment.yml
3. Use the path to this environment when you create the Giotto instructions or Giotto object

for OSX:


for linux:


for windows:



2. errors on MacOS

Some of the errors outlined below might arise because of issues with building Giotto from source.
The Giotto branch cless is a version of Giotto without C++ code, which should fix many of the installation errors.


2.1 issue 1: clang error

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
# comment out first line 'CC= ... if there are errors with compiling a package
CC=/usr/local/opt/llvm/bin/clang -fopenmp

# Also potentially CXX11 (for C++11 compiler)

# -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

2.2 issue 2: clang error

If you see this error on your MacOS:

Error message: 
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang-9: error: linker command failed with exit code 1 (use -v to see invocation)

solution: Installing the latest version of gofortran. https://github.com/fxcoudert/gfortran-for-macOS/releases/download/8.2/gfortran-8.2-Mojave.dmg

Reference: https://stackoverflow.com/questions/35999874/mac-os-x-r-error-ld-warning-directory-not-found-for-option “I am having Mac OS Catalina and in my case installation of Homebrew, the newest gcc and Gfortran 8.2.0 solved the issue.” – Magda Orzechowska “This worked for me in Mac OS Catalina as well! I used the gfortran 8.2 Mojave installation github.com/fxcoudert/gfortran-for-macOS/releases” – Danny

2.3 issue 3 (R 3.6.3 and MacOS Catalina)

If you use the latest MacOS ‘Catalina’ and the latest R version 3.6.3 then you need to install Clang 7.0.0 and GNU Fortran 6.1 as per instructions.

Additionally, you might have to specify some flags in “~/.R/Makevars”

# clang: start
CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
# clang: end

We hope that these issues will be resolved soon.

3. ‘Make’ not found error on windows

If you encounter this error:

Error in system(cmd) : (converted from warning) ‘make’ not found

Install the necessary package development tools.

## make sure Rtools is visible (from within R)
## you can set the paths manually
Sys.setenv(PATH = paste("C:/Rtools/bin","C:/Rtools/mingw_64/bin", Sys.getenv("PATH"), sep=";"))
Sys.setenv(BINPREF = "C:/Rtools/mingw_$(WIN)/bin/")

4. Error converted from warning

If you encounter this or similar error:

Error: Failed to install 'Giotto' from GitHub:
  (converted from warning) ...
  • make sure Rtools is installed, see point 3
## avoid converting warnings to errors by setting this environment variable to true (from within R)

library(devtools) # if not installed do install.package('devtools')
library(remotes) # if not installed do install.package('remotes')
remotes::install_github("RubD/Giotto", build_vignettes = F)