diff --git a/R/utils/install_packages.R b/R/utils/install_packages.R index bbb7236..b356a88 100755 --- a/R/utils/install_packages.R +++ b/R/utils/install_packages.R @@ -1,106 +1,114 @@ - - - -# 先确保 remotes 包已经安装 Make sure the remotes package is installed first -if (!requireNamespace("remotes", quietly = TRUE)) { - suppressMessages(install.packages("remotes", quiet = TRUE)) -} -if (!requireNamespace("BiocManager", quietly = TRUE)) { - suppressMessages(install.packages("BiocManager", quiet = TRUE)) -} - -if (!requireNamespace("pacman")) { - suppressMessages(install.packages("pacman", quiet = TRUE)) -} - - +# 设置 CRAN 仓库 +r <- getOption("repos") +r["CRAN"] <- "http://cran.us.r-project.org" +options(repos = r) options(install.packages.compile.from.source = "always") - -installed_packages <- character(0) -failed_packages <- character(0) - -##################################### BiocManager ##################################### -check_and_install_bioc <- function(package_name) { - - # 如果包没有安装，尝试用BiocManager来安装 If the package is not installed, try to install it using BiocManager - if (requireNamespace(package_name, quietly = TRUE)) { - installed_packages <<- c(installed_packages, package_name) - } else { - # 如果包未安装，尝试安装 If the package is not installed, try to install - tryCatch({ - # 使用BiocManager来安装包 Use BiocManager to install the package - suppressMessages(BiocManager::install(package_name, ask = FALSE)) - - # 检查是否安装成功 Check if installation was successful - if (requireNamespace(package_name, quietly = TRUE)) { - installed_packages <<- c(installed_packages, package_name) - } else { - failed_packages <<- c(failed_packages, package_name) - message(paste("Installation of", package_name, "from", repo, "failed.")) - } - }, - error = function(e) { - failed_packages <<- c(failed_packages, package_name) - message(paste("Installation of", package_name, "from", repo, "failed.")) - }) +################################ install basic packages ################################# +# 1. remotes and devtools +# 2. BiocManager +# 3. pak +# 定义一个辅助函数来安装包并在失败时终止程序 +install_and_check_func <- function(package) { + if (!requireNamespace(package, quietly = TRUE)) { + suppressMessages(install.packages(package, quiet = TRUE)) + if (!requireNamespace(package, quietly = TRUE)) { + stop(paste("Failed to install", package, ". Terminating the program.")) + } } } - -repos <- c("rtracklayer") - -for (repo in repos) { - check_and_install_bioc(repo) +# 安装 devtools remotes 和 BiocManager 包 +install_and_check_func("devtools") +install_and_check_func("remotes") +install_and_check_func("BiocManager") + +# 尝试安装 pak 包 +if (!requireNamespace("pak", quietly = TRUE)) { + suppressMessages(install.packages("pak", quiet = TRUE)) + if (!requireNamespace("pak", quietly = TRUE)) { + suppressMessages(remotes::install_github("r-lib/pak")) + if (!requireNamespace("pak", quietly = TRUE)) { + stop("Failed to install pak from both CRAN and GitHub. Terminating the program.") + } + } } -##################################### Github ##################################### +################################ install function ################################# +install_package_func <- function(package_name) { + # 提取包名：如果包名包含 '/', 提取斜线后的部分 + package_name_to_check <- ifelse(grepl("/", package_name), sub(".*/", "", package_name), package_name) -# 创建一个函数来检查和安装包 Create a function to check and install packages -check_and_install <- function(repo, ...) { - package_name <- unlist(strsplit(repo, "/"))[2] + # 检查包是否已经安装 + if (requireNamespace(package_name_to_check, quietly = TRUE)) { + return(TRUE) + } - # 如果包已经安装，直接添加到installed_packages If the package is already installed, add it to installed_packages - if (requireNamespace(package_name, quietly = TRUE)) { - installed_packages <<- c(installed_packages, package_name) - } else { - # 如果包未安装，尝试安装 If the package is not installed, try to install + # 定义一个列表，包含尝试安装包的不同函数 + install_functions <- list( + bio_install = function() suppressMessages(BiocManager::install(package_name, ask = FALSE)), + devtools_install = function() suppressMessages(devtools::install_github(package_name, quiet = TRUE)), + remotes_install = function() suppressMessages(remotes::install_github(package_name, quiet = TRUE)), + normal_install = function() suppressMessages(install.packages(package_name, repos = "https://cran.r-project.org", dependencies = TRUE, type = "source", quiet = TRUE)), + pak_install = function() suppressMessages(pak::pak(package_name)) + ) + + # 遍历安装函数，尝试安装包 + for (install_func in install_functions) { tryCatch({ - suppressMessages(remotes::install_github(repo, ...)) + install_func() - # 检查是否安装成功 Check if installation was successful + # 检查是否安装成功 if (requireNamespace(package_name, quietly = TRUE)) { - installed_packages <<- c(installed_packages, package_name) - } else { - failed_packages <<- c(failed_packages, package_name) - message(paste("Installation of", package_name, "from", repo, "failed.")) + return(TRUE) # 成功安装，返回 TRUE } - }, - error = function(e) { - failed_packages <<- c(failed_packages, package_name) - message(paste("Installation of", package_name, "from", repo, "failed.")) - }) + }, error = function(e) {}) } + # 所有方法尝试完毕，安装失败 + return(FALSE) } -repos <- c("daattali/shinydisconnect", - "RinteRface/fullPage", - "dreamRs/shinybusy", - "merlinoa/shinyFeedback", - "daattali/shinycssloaders", - "dreamRs/shinyWidgets") - -for (repo in repos) { - if (repo == "merlinoa/shinyFeedback") { - check_and_install(repo, build_vignettes = TRUE) - } else { - check_and_install(repo) - } -} - -################################ install.packages ################################ -# Used packages -packages <- c( +################################ installation ################################ +# bio +packages_bio <- c("rtracklayer", "DESeq2", "WGCNA", "GEOqueary", "limma", "edgeR", + "GSEABase", "clusterProfiler", "ConsensusClusterPlus", "GSVA", + "pheatmap", "scFeatureFilter", "AUCell", "ComplexHeatmap") + +# normal packages +packages_normal <- c( + "future", + "qs", + "ddpcr", + "rlang", + "pander", + "pacman", + "pagoda2", + "eulerr", + "Hmisc", + "pryr", + "plotly", + "enrichplot", + "RcppRoll", + "msigdbr", + "xlsxjars", + "shiny", + "svglite", + "pak", + "devtools", + "av", + "magick", + "systemfonts", + "textshaping", + "rsvg", + "gapminder", + "qpdf", + "tesseract", + "pdftools", + "ragg", + "stringr", + "usethis", + "httpuv", + "Seurat", "bslib", # Bootstrap themes and styles "data.table", # efficient handling of large datasets "DT", # interactive data tables @@ -120,6 +128,7 @@ packages <- c( "rintrojs", # interactive tour integration "rjson", # Converts R object into JSON objects and vice-versa "shiny", # creation of interactive web applications + "rJava", "shinyBS", # Bootstrap styling "shinybusy", # Automated (or not) busy indicator for Shiny apps & other progress / notifications tools "shinydashboard", # creation of dashboard-style Shiny apps @@ -137,36 +146,65 @@ packages <- c( "xfun", # Xie Yihui's functions "zip" # creation and extraction of ZIP files ) +# pak packages +pak_packages <- c("r-lib/ragg", "r-lib/usethis", "r-lib/rlang") +# github +packages_github <- c( + "daattali/shinydisconnect", + "RinteRface/fullPage", + "dreamRs/shinybusy", + "merlinoa/shinyFeedback", + "daattali/shinycssloaders", + "dreamRs/shinyWidgets", + "r-lib/textshaping", + "r-lib/systemfonts", + "jhrcook/ggasym", + "rpremrajGit/mailR", + "r-lib/textshaping", + "rstudio/httpuv", + "r-rust/gifski", + "jhrcook/ggasym", + "satijalab/seurat-data", + "satijalab/azimuth", + "satijalab/seurat-wrappers", + "stuart-lab/signac", + "satijalab/seurat", + "jhrcook/ggasym", + "kharchenkolab/pagoda2", + "NMikolajewicz/scMiko") +installed_packages <- character(0) +failed_packages <- character(0) + +packages <- c(packages_bio, packages_github, pak_packages, packages_normal) for (package in packages) { - if (suppressMessages(require(package, character.only = TRUE))) { - installed_packages <- c(installed_packages, package) + flag <- install_package_func (package) + if (flag) { + installed_packages <- c(installed_packages, package) } else { - tryCatch( - { - # 使用suppressMessages来禁止install.packages的消息 - suppressMessages(install.packages(package, repos = "https://cran.r-project.org", dependencies = TRUE, type = "source")) - - if (suppressMessages(require(package, character.only = TRUE))) { - installed_packages <- c(installed_packages, package) - } else { - failed_packages <- c(failed_packages, package) - # 这里的消息仍然会显示 - message(paste("Installation of", package, "failed.")) - } - }, - error = function(e) { - failed_packages <- c(failed_packages, package) - # 这里的消息仍然会显示 - message(paste("Installation of", package, "failed.")) - } - ) + failed_packages <- c(failed_packages, package) } } +for (package in packages) { + flag <- install_package_func (package) + if (flag) { + installed_packages <- c(installed_packages, package) + } else { + failed_packages <- c(failed_packages, package) + } +} -############################## Installation summary ############################ +for (package in packages) { + flag <- install_package_func (package) + if (flag) { + installed_packages <- c(installed_packages, package) + } else { + failed_packages <- c(failed_packages, package) + } +} +############################## summary ############################ # Print installed packages cat("The installed packages are as follows:\n") print(sort(installed_packages)) diff --git a/data/configure/nginx_pmet b/data/configure/nginx_pmet new file mode 100644 index 0000000..521a20d --- /dev/null +++ b/data/configure/nginx_pmet @@ -0,0 +1,9 @@ +# /etc/nginx/sites-available/pmet_result +server { + listen 127.0.0.1:84; + server_name 127.0.0.1; + access_log /var/log/nginx/localhost.access.log; + location /result { + alias /home/shiny/pmet/result; + } +} diff --git a/data/configure/rstudio_server_rserver.conf b/data/configure/rstudio_server_rserver.conf new file mode 100644 index 0000000..0f58b5f --- /dev/null +++ b/data/configure/rstudio_server_rserver.conf @@ -0,0 +1,5 @@ +# /etc/rstudio/rserver.conf + +# Server Configuration File +www-address=127.0.0.1 +www-port=7878 \ No newline at end of file diff --git a/data/configure/shiny-server.conf b/data/configure/shiny-server.conf new file mode 100644 index 0000000..0a004e2 --- /dev/null +++ b/data/configure/shiny-server.conf @@ -0,0 +1,24 @@ +# /etc/shiny-server/shiny-server.conf + +# Instruct Shiny Server to run applications as the user "shiny" +run_as shiny; + +# Define a server that listens on port 3838 +server { + listen 4949 127.0.0.1; + # listen 3838; + + # Define a location at the base URL + location / { + app_idle_timeout 0; + # Host the directory of Shiny Apps stored in this directory + site_dir /srv/shiny-server; + + # Log all Shiny output to files in this directory + log_dir /var/log/shiny-server; + + # When a user visits the base URL rather than a particular application, + # an index of the applications available in this directory will be shown. + directory_index on; + } +} \ No newline at end of file