![]() ![]() 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/monocle3' ) Next, install a few Bioconductor dependencies that aren't automatically installed: BiocManager :: install ( c ( 'BiocGenerics', 'DelayedArray', 'DelayedMatrixStats', 'limma', 'lme4', 'S4Vectors', 'SingleCellExperiment', 'SummarizedExperiment', 'batchelor', 'HDF5Array', 'terra', 'ggrastr' )) To install Bioconductor, open R and run: if ( ! requireNamespace ( "BiocManager", quietly = TRUE )) install.packages ( "BiocManager" ) BiocManager :: install ( version = "3.14" ) Monocle3 1.2.7 or higher to have access to the latest features. ![]()
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