Issue 46774: Remove Ruminex package references from Luminex transform script

.gitattributes

@@ -11,9 +11,8 @@ gradle/wrapper/gradle-wrapper.properties -text
 /install-flowStats.R -text
 /install-flowWorkspace.R -text
 /install-knitr.R -text
-/install-medimmune-dependencies.R -text
 /install-rlabkey-dependencies.R -text
-/install-ruminex-dependencies.R -text
+/install-luminex-dependencies.R -text
 /install-survival.R -text
 /install-util.R -text
 /readme.txt -text

test/build.gradle

@@ -35,34 +35,12 @@ project.tasks.register("installRLabKey", CopyAndInstallRPackage) {
         }
 }
 
-project.tasks.register("installRuminex", InstallRPackage) {
+project.tasks.register("installLuminexDependencies",InstallRPackage) {
     InstallRPackage task ->
         task.group = GroupNames.DEPLOY
-        task.description = "Install Ruminex and its dependencies"
-        task.packageNames = ["Ruminex"]
-        task.installScript = "install-ruminex-dependencies.R"
-        task.doLast {
-            project.copy {
-                CopySpec copy ->
-                    copy.from project.projectDir
-                    copy.into(rLibsUserPath)
-                    copy.include("Ruminex*.tar.gz")
-                    copy.rename("Ruminex.*.tar.gz", "Ruminex.tar.gz")
-            }
-            ant.exec(
-                    executable: InstallRPackage.getRPath(),
-                    dir: rLibsUserPath,
-                    failifexecutionfails: true,
-                    searchpath: true,
-                    output: "${rLibsUserPath}/logs/ruminex2.log",
-                    logError: true,
-                    append: true
-            )
-                    {
-                        // `--no-multiarch` is a workaround for TeamCity build error: "ERROR: loading failed for 'i386'"
-                        arg(line: "CMD INSTALL --no-multiarch -l ${rLibsUserPath} ${rLibsUserPath}/Ruminex.tar.gz")
-                    }
-        }
+        task.description = "Install Luminex Dependencies packages"
+        task.packageNames = ["luminex"]
+        task.installScript = "install-luminex-dependencies.R"
 }
 
 project.tasks.register("installKnitr",InstallRPackage) {
@@ -82,15 +60,6 @@ project.tasks.register("installEhrDependencies",InstallRPackage) {
 }
 
 
-project.tasks.register("installMedimmuneDependencies", InstallRPackage) {
-    InstallRPackage task ->
-        task.group = GroupNames.DEPLOY
-        task.description = "Install MedImmune dependencies"
-        task.packageNames = ["doBy", "gdata", "jsonlite", "openxlsx", "tidyr", "xml2"]
-        task.installScript = "install-medimmune-dependencies.R"
-}
-
-
 project.tasks.register("installRSurvival", InstallRPackage) {
     InstallRPackage task ->
         task.group = GroupNames.DEPLOY
@@ -105,7 +74,7 @@ project.tasks.register("install") {
         task.description = "Install R packages"
         task.dependsOn(
                 project.tasks.installRLabKey,
-                project.tasks.installRuminex,
+                project.tasks.installLuminexDependencies,
                 project.tasks.installKnitr,
                 project.tasks.installEhrDependencies,
                 project.tasks.installRSurvival

test/install-ruminex-dependencies.R → test/install-luminex-dependencies.R

@@ -1,12 +1,12 @@
 ##
-#  Copyright (c) 2010 LabKey Corporation
-# 
+#  Copyright (c) 2013 LabKey Corporation
+#
 #  Licensed under the Apache License, Version 2.0 (the "License");
 #  you may not use this file except in compliance with the License.
 #  You may obtain a copy of the License at
-# 
+#
 #      http://www.apache.org/licenses/LICENSE-2.0
-# 
+#
 #  Unless required by applicable law or agreed to in writing, software
 #  distributed under the License is distributed on an "AS IS" BASIS,
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -20,4 +20,4 @@ if (OS.type == "unix") {
     # Workaround for https://github.com/jyypma/nloptr/issues/40
     install.dependencies("nloptr", github_deps=c("jyypma/nloptr"))
 }
-install.dependencies("Ruminex", c("drc", "xtable", "alr3", "Cairo", "plotrix"))
+install.dependencies("luminex", c("drc", "xtable", "Cairo", "plotrix"))

test/readme.txt

@@ -1,5 +1 @@
 Rpackages to be installed by tests.
-
-Ruminex:
-Available at: http://labs.fhcrc.org/fong/Ruminex/index.html
-