8. Installation troubleshooting

Here, we summarise the installation errors that have been reported for BASiCS. If you encounter any other issues, please let us know so that we can update this information.

Rcpp cannot be installed (MacOS)

Solution: check this repository.

gfortran error

If you are unable to install BASiCS in a Mac OS X system, you might require an additional gfortran library.

• If you are running R versions 3.0.0 - R 3.3.0, this can be installed in the Mac terminal using the following command:

curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /

• If you are running R 3.4.0 (or above), you should install the official gfortran binary for your OS (e.g. El Capitan) from here.

Another option is to use the macrtools library which can do the installation for you. You can find it here. Here is the code that I used following their instructions.

# Installation
install.packages("remotes")
remotes::install_github("rmacoslib/macrtools")
library(macrtools)

# Check if required dependencies are installed
is_xcode_cli_installed() 
is_gfortran_installed() 

# Install the required dependencies (may take a while depending on what is needed)
macos_rtools_install()

# Check again if required dependencies are installed
is_xcode_cli_installed()
is_gfortran_installed()

# Done!

pandoc error

If you are not using RStudio, you might need to manually install pandoc in order to create the vignette provided for BASiCS

Installation using R-devel

These are some of the issues I had after installing R-devel (3.5)

1. Problem: clang: error: unsupported option '-fopenmp' when installing data.table. Solution. Also here
2. Problem: 'openssl/ssl.h' file not found when installing git2r. Solution.

brew install openssl

Problems after updating MacOS to High Sierra

After a search through various Github issues and Stack Overflow posts, the following solution did the job. First, download and install the latest version of R studio. Then run the following in the command line (WARNING: I HAD TO RE-INSTALL MOST OF MY R LIBRARIES AFTER DOING THIS!)

brew install gcc
brew update && brew reinstall r
brew link --overwrite r
brew install openssl
brew install libgit2

Other reported issues

Additional installation issues/solutions:

• Issue 9