docs/documentation/02_installation.md

In YingMa1993/CARD: Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

layout: page title: Installation description: ~

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.

YingMa1993/CARD documentation built on Feb. 14, 2024, 12:24 p.m.