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addAllostericEdges <- function(allostericEdges, networkSUID,
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                               targetlayer = "kegg_global"){
 
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    allostericTable = read.table(allostericEdges)
 
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
	<properties>
		<cytoscape.api.version>3.6.0</cytoscape.api.version>

		<maven-compiler-plugin.version>3.6.1</maven-compiler-plugin.version>
		<maven-bundle-plugin.version>5.1.1</maven-bundle-plugin.version>

		<osgi.api.version>4.2.0</osgi.api.version>

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Create A Package (パッケージを作る)

A package is a collection of functions that work together in a cohesive manner to achieve a goal. It (should) include detailed documentation through man pages and vignettes and (should) be tested for accuracy and efficiency. Writing R extensions is a very detailed manual provided by CRAN that explains writing packages and what the structure of a package should look like. This vignette is going to walk you through making your first package in RStudio as well as how to submitt a package to Bioconductor.

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KEGG_GLOBAL_PATHWAY_IDS <- c("01100", "01110", "01120", "01200", "01210",
                             "01212", "01230", "01220")

importLayer <- function(networkFilePath){
    fileExtension <- tools::file_ext(networkFilePath)
    if (fileExtension %in% c("sif", "gml", "xgmml", "xml")){
        message("Importing ", networkFilePath)
        suID <- RCy3::importNetworkFromFile(file = paste(getwd(), "/",
                                                    networkFilePath, sep=""))
        Sys.sleep(3)

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I replaced devtools::install_github to BiocManager::install.

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library(dash)
library(dashHtmlComponents)
library(dashCytoscape)
library(readr)
library(purrr)
library(dplyr)

app <- Dash$new()

nodes <- read_csv("C:/Users/kozon/Downloads/nodes.csv")

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Install software in Google Colab

!apt install xfce4 xfce4-goodies vnc4server htop
!pip install pyngrok
!pip install git+https://github.com/bdemchak/py4cytoscape
!wget https://github.com/cytoscape/cytoscape/releases/download/3.8.0/cytoscape-unix-3.8.0.tar.gz
!tar xf cytoscape-unix-3.8.0.tar.gz

# configure VNC and xfce4
!mkdir ~/.vnc

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# library(testthat)
# testthat::with_mock(
#     get_node_table = function(x) {
#         transomics2cytoscape:::getNodeTableWithZheight(
#             transomics2cytoscape:::importKgml(x))
#     },
#     expect_equal(dim(get_node_table("rno00010"))[1], 100)
# )

testthat::with_mock(

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on:
  push:

name: R-CMD-check

jobs:
  R-CMD-check:
    runs-on: ${{ matrix.config.os }}
    container: ${{ matrix.config.image }}