diff --git a/.gitattributes b/.gitattributes index 8b06251..6a8958d 100644 --- a/.gitattributes +++ b/.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 diff --git a/test/build.gradle b/test/build.gradle index 9ebba11..6f6cb31 100644 --- a/test/build.gradle +++ b/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 diff --git a/test/install-ruminex-dependencies.R b/test/install-luminex-dependencies.R similarity index 85% rename from test/install-ruminex-dependencies.R rename to test/install-luminex-dependencies.R index 38ca546..7a88a48 100644 --- a/test/install-ruminex-dependencies.R +++ b/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")) \ No newline at end of file diff --git a/test/install-medimmune-dependencies.R b/test/install-medimmune-dependencies.R deleted file mode 100644 index c876102..0000000 --- a/test/install-medimmune-dependencies.R +++ /dev/null @@ -1,18 +0,0 @@ -## -# Copyright (c) 2016-2017 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. -# See the License for the specific language governing permissions and -# limitations under the License. -## - -source("install-util.R") -install.dependencies("MedImmune", c("doBy", "gdata", "jsonlite", "openxlsx", "tidyr", "xml2")) diff --git a/test/readme.txt b/test/readme.txt index 4dd484b..9cd3713 100644 --- a/test/readme.txt +++ b/test/readme.txt @@ -1,5 +1 @@ Rpackages to be installed by tests. - -Ruminex: -Available at: http://labs.fhcrc.org/fong/Ruminex/index.html -