In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

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
channels:
 — defaults
dependencies:
 — 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:

python conda env create -f environment.yml

3. Use the path to this environment when you create the Giotto instructions or Giotto object

for OSX:

/Users/your_username/anaconda3/envs/giotto_env/bin/pythonw

for linux:

/Users/your_username/anaconda3/envs/giotto_env/bin/python

for windows:

/Users/your_username/anaconda3/envs/giotto_env/python.exe

\

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.

remotes::install_github("RubD/Giotto@cless") 

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 ```{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

### 2.2 issue 2: clang error

If you see this error on your MacOS: 
```{bash, eval = FALSE}
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"

```{bash, eval = FALSE}

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

Solution:
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)
Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS"=TRUE)

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)

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.