Merge pull request #2 from nmfs-fish-tools/debug-rcmdcheck

changes to r pkg, and cmake file

.Rbuildignore

@@ -1,3 +1,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.github$
+^README\.md$
+^\.devcontainer$

.devcontainer/devcontainer.json

@@ -1,13 +1,55 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.234.0/containers/r
 {
-    "name": "my-project-devcontainer",
-    "image": "mcr.microsoft.com/devcontainers/base:ubuntu",  // Any generic, debian-based image.
-    "features": {
-        "ghcr.io/devcontainers/features/go:1": {
-            "version": "1.18"
-        },
-        "ghcr.io/devcontainers/features/docker-in-docker:1": {
-            "version": "latest",
-            "moby": true
-        }
-    }
+	"name": "R (rocker/r-ver base)",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"image": "ghcr.io/rocker-org/devcontainer/r-ver:4.3", //commma needed if other sections are used.
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	"features": {
+		// if we want to install r packages using pak
+		// more info: https://github.com/rocker-org/devcontainer-features/blob/main/src/r-packages/README.md
+		"ghcr.io/rocker-org/devcontainer-features/apt-packages:1": {
+			"packages": "make,gcc,g++,cmake,clang-tidy,clang-format,clang,doxygen,libxtst6,libxt6"			
+		},
+		 "ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
+			"packages": "methods,Rcpp,RInside,BH",
+			 "installSystemRequirements": true
+		  }
+		},
+	// // if we want quarto cli
+	     // more info: https://github.com/rocker-org/devcontainer-features/blob/main/src/quarto-cli/README.md
+	//    "ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {}
+	// },
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	"postCreateCommand": "echo 'options(repos = c(CRAN = \"https://cloud.r-project.org\"))' | sudo sh -c 'cat - >>\"${R_HOME}/etc/Rprofile.site\"'",
+
+	// Configure tool-specific properties.
+	 "customizations": {
+	   "vscode": {
+	 		// Set *default* container specific settings.json values on container create.
+	 		// Add the IDs of extensions you want installed when the container is created.
+	 		"extensions": [
+		        // if we want liveshare.
+	 			"ms-vsliveshare.vsliveshare",
+				"ms-vscode.cpptools",
+				 "ms-vscode.cmake-tools",
+				 "GitHub.codespaces",
+				 "bbenoist.Doxygen",
+				 "matepek.vscode-catch2-text-adapter",
+				 "hbenl.vscode-test-explorer",
+				 "reditorsupport.r",
+				 "rdebugger.r-debugger",
+                                 "github.vscode-pull-request-github"
+	 		]
+	     }
+
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
 }
+}

.github/.gitignore

@@ -1 +1 @@
-*.html
+*.html

.gitignore

@@ -5,3 +5,6 @@
 src/*.o
 src/*.so
 src/*.dll
+_builds/
+_install/
+.DS_Store

CMakeLists.txt

@@ -64,7 +64,14 @@ ELSEIF(EXISTS ${R_USER}/Rcpp)
  SET(RCPP_INCLUDE ${RCPP_HOME}/include)
  include_directories("${RCPP_INCLUDE}")
  SET(_LIB_RCPP ${RCPP_HOME}/libs/Rcpp.so)
-
+
+ELSEIF(EXISTS ${R_HOME}/site-library/Rcpp)
+
+  SET(RCPP_HOME ${R_HOME}/site-library/Rcpp)
+  SET(RCPP_INCLUDE ${RCPP_HOME}/include)
+  include_directories("${RCPP_INCLUDE}")
+  SET(_LIB_RCPP ${RCPP_HOME}/libs/Rcpp.so)
+
 ELSE()
  MESSAGE(FATAL_ERROR  "Package Rcpp not found at ${R_HOME} or ${R_USER}")
 ENDIF()
@@ -82,12 +89,17 @@ ELSEIF(EXISTS ${R_USER}/BH)
  SET(BOOST_HOME ${R_USER}/BH)
  SET(BOOST_INCLUDE ${BOOST_HOME}/include)
  include_directories("${BOOST_INCLUDE}")
+
+ELSEIF(EXISTS ${R_HOME}/site-library/BH)
+
+ SET(BOOST_HOME ${R_HOME}/site-library/BH)
+ SET(BOOST_INCLUDE ${BOOST_HOME}/include)
+ include_directories("${BOOST_INCLUDE}")
 
 ELSE()
  MESSAGE(FATAL_ERROR "Package BH not found")
 ENDIF()
 
-
 SET(LIB_DIR ${CMAKE_INSTALL_PREFIX}/libs)
 file(MAKE_DIRECTORY ${LIB_DIR})
 
@@ -111,7 +123,7 @@ link_directories(${R_HOME}/lib)
 include(GenerateExportHeader)
 include_directories("${CMAKE_CURRENT_BINARY_DIR}") 
 
-add_library(processR SHARED src/processR.cpp)
+add_library(processR SHARED src/ProcessR.cpp)
 generate_export_header(processR)
 
 

DESCRIPTION

@@ -1,18 +1,22 @@
 Package: processR
-Type: Package
 Title: Concurrent processing in R
 Version: 1.0
-Date: 2023-09-15
-Author: Matthew Supernaw
-Maintainer: Matthew Supernaw <[email protected]>
+Authors@R:
+    person("Matthew", "Supernaw", , "[email protected]", role = c("aut", "cre"))
 Description: A multi-process package for R.
 License: GPL (>= 2)
+URL: https://github.com/nmfs-fish-tools/processR
+BugReports: https://github.com/nmfs-fish-tools/processR/issues
 Depends:
-    R (>= 4.0)
+    R (>= 4.0.0)
 Imports: 
-      Rcpp (>= 1.0.10), 
-      methods, 
-      RInside, 
-      BH
-LinkingTo: Rcpp, RInside
+    BH,
+    methods,
+    Rcpp (>= 1.0.10),
+    RInside
+LinkingTo: 
+    Rcpp,
+    RInside
+Encoding: UTF-8
 RoxygenNote: 7.2.3
+SystemRequirements: C++17