Get peer building on a modern system, R libraries included

.github/workflows/build.yml

@@ -0,0 +1,40 @@
+# This starter workflow is for a CMake project running on a single platform. There is a different starter workflow if you need cross-platform coverage.
+# See: https://github.com/actions/starter-workflows/blob/main/ci/cmake-multi-platform.yml
+name: CMake on a single platform
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: Release
+
+jobs:
+  build:
+    # The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
+    # You can convert this to a matrix build if you need cross-platform coverage.
+    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+
+    - uses: r-lib/actions/setup@v2
+      with:
+        r-version: '4.3.3'
+
+    - name: Configure CMake
+      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
+      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
+      run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
+
+    - name: Build
+      # Build your program with the given configuration
+      run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}

R/CMakeLists.txt

@@ -12,7 +12,7 @@ if (BUILD_R_PACKAGE)
 
   find_package(Eigen3 REQUIRED)
   link_libraries(Eigen3::Eigen)
-  
+
   include_directories(${PEER_SRC_DIR}/External/alglib)
   include_directories(${PEER_SRC_DIR}/include)
 
@@ -28,36 +28,42 @@ if (BUILD_R_PACKAGE)
   set_source_files_properties(peer.i PROPERTIES CPLUSPLUS ON)
   set_source_files_properties(peer.i PROPERTIES SWIG_FLAGS "-includeall")
   set_source_files_properties(peer.i PROPERTIES SWIG_FLAGS "-cpperraswarn")
-  swig_add_module(peer r peer.i)
-  swig_link_libraries(peer ${SWIGLINKLIBS})
+  swig_add_module(r-peer r peer.i)
+  swig_link_libraries(r-peer ${SWIGLINKLIBS})
 
   ADD_CUSTOM_COMMAND(
-    TARGET peer POST_BUILD
+    TARGET r-peer POST_BUILD
     COMMAND ${CMAKE_COMMAND} -E copy_directory
        ${PEER_SOURCE_DIR}/R/peer 
        ${PEER_SOURCE_DIR}/build/R/peer)
 
   ADD_CUSTOM_COMMAND(
-    TARGET peer POST_BUILD
+    TARGET r-peer POST_BUILD
     COMMAND ${CMAKE_COMMAND} -E copy
-       ${PEER_SOURCE_DIR}/build/R/peerR_wrap.cxx
+       ${PEER_SOURCE_DIR}/build/R/CmakeFiles/r-peer.dir/peerR_wrap.cxx
        ${PEER_SOURCE_DIR}/build/R/peer/src/peerR_wrap.cpp)
 
   ADD_CUSTOM_COMMAND(
-    TARGET peer POST_BUILD
+    TARGET r-peer POST_BUILD
     COMMAND ${CMAKE_COMMAND} -E copy
        ${PEER_SOURCE_DIR}/build/R/peer.R
        ${PEER_SOURCE_DIR}/build/R/peer/R/peer.R)
 
+  # CMAKE was putting a --jobserver-auth-string into MAKEFLAGS that breaks R CMD INSTALL
+
   if (BUILD_UNIVERSAL)
     ADD_CUSTOM_COMMAND(
-      TARGET peer POST_BUILD
-      COMMAND R CMD INSTALL --build ${PEER_SOURCE_DIR}/build/R/peer
+      TARGET r-peer POST_BUILD
+      COMMAND MAKEFLAGS=-j8 R CMD INSTALL --build ${PEER_SOURCE_DIR}/build/R/peer
       COMMENT "Building and installing the peer R package")
   else (BUILD_UNIVERSAL)
     ADD_CUSTOM_COMMAND(
-      TARGET peer POST_BUILD
-      COMMAND R CMD INSTALL --no-multiarch --build ${PEER_SOURCE_DIR}/build/R/peer
+      TARGET r-peer POST_BUILD
+      COMMAND env
+      COMMENT "print env")
+    ADD_CUSTOM_COMMAND(
+      TARGET r-peer POST_BUILD
+      COMMAND MAKEFLAGS=-j8 R CMD INSTALL --no-multiarch --build ${PEER_SOURCE_DIR}/build/R/peer
       COMMENT "Building and installing the peer R package")
   endif (BUILD_UNIVERSAL)
 

R/Makefile

@@ -6,7 +6,7 @@ all: peer_wrap.cpp
 	R CMD SHLIB peer_wrap.cpp
 
 peer_wrap.cpp: peer.i
-	swig -c++ -r -o peer_wrap.cpp -I../include -I../External -I.. peer.i
+	swig -c++ -r -o peer_wrap.cpp -I../include -I.. peer.i
 
 clean:
 	$(RM) ./peer_wrap.so

R/Makevars

@@ -1,2 +1,2 @@
 PKG_LIBS=-L./lib -lpeer
-PKG_CPPFLAGS= -I ./../External -I .. -DSWIG
+PKG_CPPFLAGS=-I.. -DSWIG

R/peer/src/Makevars

@@ -1,2 +1,2 @@
 PKG_LIBS=-L./../../../src -lpeerlib -L./../../../External/alglib/src -lalglib
-PKG_CPPFLAGS=-I./../../../../include -I./../../../../External/alglib -I./../../../../External/alglib/src -I./../../../../External -DSWIG
+PKG_CPPFLAGS=-I./../../../../include -I./../../../../External/alglib -I./../../../../External/alglib/src -I"${CONDA_PREFIX}"/include/eigen3 -DSWIG

cmake/FindR.cmake

@@ -1,3 +1,8 @@
+
+if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+  set(CMAKE_FIND_APPBUNDLE "LAST")
+endif()
+
 # find the R binary
 
 MESSAGE(STATUS "Looking for R executable")