usr/local/bin/gfortran) you have a previous installation of gfortran that needs to be removed. For this, you can launch a terminal window and type 'which gfortran'.

Remove other gfortran installations if they exist.

Make sure that you have Xcode command line tools installed on your computer.

The above error indicates that you need to install gfortran on your computer (for Mac users only). Make: *** Error 1ĮRROR: compilation failed for package 'leidenbase' Solution: Restart the Monocle 3 installation instructions.Įrrors involving gfortran: Example error messages: make: gfortran: No such file or directory Xcode-select -install and then follow the prompts. Install it on your system, see the sf installation instructions here.įor Mac users only, Xcode command line tools is required. One of Monocle 3's dependencies requires a package called gdal. Installation of package ‘sf’ had non-zero exit status Solution: * removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/sf’ If you discover new difficulties, please open an issue on Github describingĮrrors involving Gdal: Example error messages: configure: error: gdal-config not found or not executable.ĮRROR: configuration failed for package ‘sf’ Library ( monocle3 ) Installation troubleshootingīelow are a few of the most common errors that users encounter when installing To ensure that Monocle 3 was installed correctly, start a new R session and If you wish to install the develop branch of monocle3, execute: devtools :: install_github ( 'cole-trapnell-lab/monocle3', ref = 'develop' ) Testing the installation Now, install monocle3 through the cole-trapnell-lab GitHub, execute: install.packages ( 'devtools' ) devtools :: install_github ( 'cole-trapnell-lab/leidenbase' ) devtools :: install_github ( 'cole-trapnell-lab/monocle3' ) Next, install a few Bioconductor dependencies that aren't automatically installed: BiocManager :: install ( c ( 'BiocGenerics', 'DelayedArray', 'DelayedMatrixStats', 'limma', 'S4Vectors', 'SingleCellExperiment', 'SummarizedExperiment', 'batchelor', 'Matrix.utils' )) To install Bioconductor, open R and run: if ( ! requireNamespace ( 'BiocManager', quietly = TRUE )) install.packages ( 'BiocManager' ) BiocManager :: install ( version = '3.10' )

Monocle3 0.2.3 or higher to have access to the latest features.

Install gfortran r