Contents

Last modified: 2021-10-11 14:34:40
Compiled: Mon Oct 11 14:40:17 2021

1 Getting started

To install agGraphSearch, start R and enter:

install.packages( "devtools" )
devtools::install_github( "kumeS/agGraphSearch" )

Once agGraphSearch is installed, it can be loaded by the following command.

library("agGraphSearch")

2 How to use Rocker environment.

Optionally, you use the following sh command on Mac/Linux Terminal if you want to use the Rocker environment.

docker run \
       -d \
       --name RStudio \
       -v $(pwd)/XXX:/home/rstudio/XXX \
       -e ROOT=TRUE \
       -e PASSWORD=PassWord \
       -p 8787:8787 \
       rocker/rstudio:4.0.5
#XXX: Your folder path

#Then, browse the page
open http://localhost:8787

An alternative way, type the R code below if you want to run the Rocker environment from the R console.

system("docker run \\
        -d \\
        --name RStudio \\
        -v $(pwd)/XXX:/home/rstudio/XXX \\
        -e ROOT=TRUE \\
        -e PASSWORD=PassWord \\
        -p 8787:8787 \\
       rocker/rstudio:4.0.5")
#XXX: Your folder path

#Then, browse the page
system("open http://localhost:8787")

See Rocker page if you want to know details to the rocker image.

2.1 Optional Rocker setting

Type the R code below for the settings.

## run first on the terminal windows
#sudo apt-get update
#sudo apt-get install libxml2-dev libglpk-dev

#Install packages
install.packages("BiocManager")
BiocManager::install("BiocStyle")

install.packages( "devtools" )
devtools::install_github( "kumeS/agGraphSearch" )
library( "agGraphSearch" )

Session information

## R version 4.1.0 (2021-05-18)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Catalina 10.15.7
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] ja_JP.UTF-8/ja_JP.UTF-8/ja_JP.UTF-8/C/ja_JP.UTF-8/ja_JP.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.20.2
## 
## loaded via a namespace (and not attached):
##  [1] bookdown_0.24       digest_0.6.27       R6_2.5.1           
##  [4] jsonlite_1.7.2      magrittr_2.0.1      evaluate_0.14      
##  [7] stringi_1.7.4       rlang_0.4.11        jquerylib_0.1.4    
## [10] bslib_0.3.0         rmarkdown_2.11      tools_4.1.0        
## [13] stringr_1.4.0       xfun_0.26           yaml_2.2.1         
## [16] fastmap_1.1.0       compiler_4.1.0      BiocManager_1.30.16
## [19] htmltools_0.5.2     knitr_1.34          sass_0.4.0