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Merge pull request #53 from MD-Anderson-Bioinformatics/v1.0.2_mary
Installation improvements
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| Type: Package | ||
| Package: NGCHM | ||
| Title: Next Generation Clustered Heat Maps | ||
| Version: 1.0.1 | ||
| Version: 1.0.2 | ||
| Authors@R: c( | ||
| person(c("Bradley", "M"), "Broom", , "[email protected]", role = "aut", | ||
| comment = c(ORCID = "0000-0002-0915-3164")), | ||
|
|
@@ -47,6 +47,7 @@ Encoding: UTF-8 | |
| Roxygen: list(markdown = TRUE) | ||
| RoxygenNote: 7.2.3 | ||
| Collate: | ||
| 'internalFunctions.R' | ||
| 'allClasses.R' | ||
| 'allGenerics.R' | ||
| 'allMethods.R' | ||
|
|
@@ -58,5 +59,5 @@ Collate: | |
| 'zzz.R' | ||
| 'package.R' | ||
| SystemRequirements: | ||
| Java (>= 8.0) | ||
| Java (>= 11) | ||
| Git | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,128 @@ | ||
| #' Check for External Utilities used by NGCHM | ||
| #' | ||
| #' This function checks for the presence of certain external programs that are suggested for the package to | ||
| #' function properly. It checks for 'git', 'scp', 'ssh', and 'tar'. If any of these programs are not found, | ||
| #' it prints a warning. | ||
| #' | ||
| #' @param None. | ||
| #' | ||
| #' @return None. This function is called for its side effects (printing warnings if necessary programs are not found). | ||
| #' | ||
| #' @noRd | ||
| #' @keywords internal | ||
| checkForExternalUtilities <- function() { | ||
| suggestedUtilities <- list( | ||
| "git" = paste0("CRITICAL WARNING: Unable to verify 'git' installation. Git is required to create NG-CHMs. ", | ||
| "Install git in order to create NG-CHMs."), | ||
| "scp" = "Missing suggested external program 'scp'. Some server functionality unavailable.", | ||
| "ssh" = "Missing suggested external program 'ssh'. Some server functionality unavailable.", | ||
| "tar" = "Missing suggested external program 'tar'. Some server functionality unavailable." | ||
| ) | ||
| for (name in names(suggestedUtilities)) { | ||
| checkResponse <- NULL | ||
| suppressWarnings(try({ | ||
| checkResponse <- system2(name, "--version", stdout = TRUE, stderr = TRUE) | ||
| }, silent = TRUE)) | ||
| if (is.null(checkResponse)) { | ||
| warning(suggestedUtilities[[name]]) | ||
| } | ||
| } | ||
| } | ||
|
|
||
| #' Check Java Version | ||
| #' | ||
| #' This function checks if the Java is installed and if the installed version meets the required version. | ||
| #' It extracts the major version number from the Java version string and compares it with the required version. | ||
| #' | ||
| #' @param requiredJavaVersion The required Java version. Default is 11 because ShaidyMapGen.jar is compiled for Java 11. | ||
| #' | ||
| #' @return Boolean value indicating if the installed Java version meets the required version. | ||
| #' | ||
| #' @noRd | ||
| #' @keywords internal | ||
| checkForJavaVersion <- function(javaExecutable = "java", requiredJavaVersion = 11) { | ||
| requiredJavaVersion <- as.integer(requiredJavaVersion) | ||
| message <- paste0("CRITICAL WARNING: Unable to verify Java installation. ", | ||
| "Java ", requiredJavaVersion, " is required to create .ngchm and .html files.\n\n", | ||
| "\tInstall Java ", requiredJavaVersion, " or higher for to create .ngchm and .html files.\n") | ||
| checkResponse <- NULL | ||
| suppressWarnings(try({ | ||
| checkResponse <- system2(javaExecutable, "--version", stdout = TRUE, stderr = TRUE) | ||
| }, silent = TRUE)) | ||
| if (is.null(checkResponse)) { # java not installed | ||
| warning(message) | ||
| return(FALSE) | ||
| } | ||
| haveVersion <- FALSE | ||
| suppressWarnings(try({ | ||
| versionNumber <- strsplit(checkResponse, split = "\\.")[[1]][1] # from first line , rm everything after first '.' | ||
| versionNumber <- as.numeric(gsub("\\D", "", versionNumber)) # rm non-digits, should be left with major version number | ||
| if (versionNumber >= requiredJavaVersion) { | ||
| haveVersion <- TRUE | ||
| } | ||
| }, silent = TRUE)) | ||
| if (!haveVersion) { # java installed, but version is less than required (or version number could not be extracted) | ||
| warning(message) | ||
| return(FALSE) | ||
| } | ||
| return(TRUE) # java installed and version is at least required version | ||
| } | ||
|
|
||
| #' Check for NGCHMSupportFiles package | ||
| #' | ||
| #' If the environment variables SHAIDYMAPGEN and NGCHMWIDGETPATH are set, we assume the user has what they need. | ||
| #' If the environment variables are not set, we check if the NGCHMSupportFiles package is installed and provide | ||
| #' user feedback. | ||
| #' | ||
| #' @param None. | ||
| #' | ||
| #' @return Boolean value. TRUE if SHAIDYMAPGEN and NGCHMWIDGETPATH are set, FALSE otherwise. | ||
| #' | ||
| #' @noRd | ||
| #' @keywords internal | ||
| checkForNGCHMSupportFiles <- function() { | ||
| SHAIDYMAPGEN <- Sys.getenv("SHAIDYMAPGEN") | ||
| NGCHMWIDGETPATH <- Sys.getenv("NGCHMWIDGETPATH") | ||
| if (nzchar(SHAIDYMAPGEN) > 0 && nzchar(NGCHMWIDGETPATH) > 0) { # SHAIDYMAPGEN and NGCHMWIDGETPATH are set | ||
| return(TRUE) | ||
| } | ||
| mary <- suppressWarnings(find.package("NGCHMSupportFiles", quiet = TRUE)) | ||
| if (length(suppressWarnings(find.package("NGCHMSupportFiles", quiet = TRUE))) > 0) { # NGCHMSupportFiles is installed | ||
| warning(paste0("WARNING: NGCHMSupportFiles package is installed but not loaded. ", | ||
| "This package is required to create .ngchm and .html files. ", | ||
| "Please load the package with command:\n\n", | ||
| "\tlibrary(NGCHMSupportFiles)\n")) | ||
| } else { | ||
| warning(paste0("CRITICAL WARNING: Package NGCHMSupportFiles is not installed. ", | ||
| "This package is required to create .ngchm and .html files. ", | ||
| "Please install and load NGCHMSupportFiles with commands: \n\n", | ||
| "\tinstall.packages('NGCHMSupportFiles', repos = c('https://md-anderson-bioinformatics.r-universe.dev', 'https://cloud.r-project.org'))\n\n", | ||
| "\tlibrary(NGCHMSupportFiles)\n")) | ||
| } | ||
| return(FALSE) | ||
| } | ||
|
|
||
| #' Check for NGCHMDemoData package | ||
| #' | ||
| #' @param None. | ||
| #' | ||
| #' @return Boolean. TRUE if NGCHMDemoData is loaded, FALSE otherwise. | ||
| #' | ||
| #' @noRd | ||
| #' @keywords internal | ||
| checkForNGCHMDemoData <- function() { | ||
| if ("package:NGCHMDemoData" %in% search()) { # NGCHMDemoData is loaded | ||
| return(TRUE) | ||
| } | ||
| if (length(suppressWarnings(find.package("NGCHMDemoData", quiet = TRUE))) > 0) { # NGCHMDemoData is installed | ||
| warning(paste0("WARNING: NGCHMDemoData package is installed but not loaded. ", | ||
| "To run examples and website vignettes, please load the package with command:\n\n", | ||
| "\tlibrary(NGCHMDemoData)\n")) | ||
| } else { | ||
| warning(paste0("NOTE: Package NGCHMDemoData is not installed. ", | ||
| "This package is used by the examples and website vignettes. Please install and load NGCHMDemoData with command: \n\n", | ||
| "\tinstall.packages('NGCHMDemoData', repos = c('https://md-anderson-bioinformatics.r-universe.dev', 'https://cloud.r-project.org'))\n\n", | ||
| "\tlibrary(NGCHMDemoData)\n")) | ||
| } | ||
| return(FALSE) | ||
| } |
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