Table of Contents
CARD
is implemented as an R package, which can be installed from GitHub by:
Dependencies #
- R version >= 4.0.0.
- R packages: SingleCellExperiment, SummarizedExperiment, concaveman, sp, Matrix, methods, ggplot2, ggcorrplot, MuSiC, fields, MCMCpack, dplyr, sf, RANN, stats, reshape2, RColorBrewe, scatterpie, grDevices, stats, nnls, pbmcapply, spatstat, gtools, RcppML, NMF
1. Install devtools
if necessary #
install.packages('devtools')
2. Install CARD
#
devtools::install_github('YMa-lab/CARD')
3. Load package #
library(CARD)
This package is supported for Windows 10, MAC and Linux. The package has been tested on the following systems:
- Windows 10: Home (1903)
- MAC: OSX (10.14.1)
- Linux: Ubuntu (16.04.6)
4. Some possible issues when installing the package, especially on the MacOS system #
(1) Cannot find tools necessary when using R in the MacOS system.
Error: Failed to install 'CARD' from GitHub:
Could not find tools necessary to compile a package
Call `pkgbuild::check_build_tools(debug = TRUE)` to diagnose the problem.
possible solution: in R, type the code options(buildtools.check = function(action) TRUE )
, see the discussion about this error, link
(2) library not found for -lgfortran when using R in the MacOS system.
ld: library not found for -lgfortran
It seems the gfortran is not well installed on the MacOS system. Please check this link for the gfortran installation to see if it helps.