Support R-package with cmake build and fix installation instructions (#…

…17228) * Support R-package with cmake build and fix installation instructions * Fix typo * Fix callback.R * Clarify creation of personal R library * Fix generation of R-package documentation * Remove unused USE_BLAS variable on CI for make rpkg * Add cmake build command for get_started/linux/r/*.md pages * Fix zzz.R swallowing error messages * Fix R-package/src/Makevars for OpenCV dependency See #17282
apache · Jan 14, 2020 · 9f2e73f · 9f2e73f
1 parent 3971938
commit 9f2e73f
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diff --git a/Makefile b/Makefile
@@ -683,36 +683,6 @@ cython3:
 cyclean:
 	rm -rf python/mxnet/*/*.so python/mxnet/*/*.cpp
 
-# R related shortcuts
-rcpplint:
-	3rdparty/dmlc-core/scripts/lint.py mxnet-rcpp ${LINT_LANG} R-package/src
-
-rpkg:
-	mkdir -p R-package/inst/libs
-	cp src/io/image_recordio.h R-package/src
-	cp -rf lib/libmxnet.so R-package/inst/libs
-
-	if [ -e "lib/libtvm_runtime.so" ]; then \
-		cp -rf lib/libtvm_runtime.so R-package/inst/libs; \
-	fi
-
-	mkdir -p R-package/inst/include
-	cp -rl include/* R-package/inst/include
-	Rscript -e "if(!require(devtools)){install.packages('devtools', repo = 'https://cloud.r-project.org/')}"
-	Rscript -e "if(!require(roxygen2)||packageVersion('roxygen2') < '6.1.1'){install.packages('roxygen2', repo = 'https://cloud.r-project.org/')}"
-	Rscript -e "library(devtools); library(methods); options(repos=c(CRAN='https://cloud.r-project.org/')); install_deps(pkg='R-package', dependencies = TRUE)"
-	cp R-package/dummy.NAMESPACE R-package/NAMESPACE
-	echo "import(Rcpp)" >> R-package/NAMESPACE
-	R CMD INSTALL R-package
-	Rscript -e "require(mxnet); mxnet:::mxnet.export('R-package'); warnings()"
-	rm R-package/NAMESPACE
-	Rscript -e "devtools::document('R-package');warnings()"
-	R CMD INSTALL R-package
-
-rpkgtest:
-	Rscript -e 'require(testthat);res<-test_dir("R-package/tests/testthat");if(!testthat:::all_passed(res)){stop("Test failures", call. = FALSE)}'
-	Rscript -e 'res<-covr:::package_coverage("R-package");fileConn<-file(paste("r-package_coverage_",toString(runif(1)),".json"));writeLines(covr:::to_codecov(res), fileConn);close(fileConn)'
-
 scalaclean:
 	(cd $(ROOTDIR)/scala-package && mvn clean)
 

diff --git a/R-package/Makefile b/R-package/Makefile
@@ -0,0 +1,33 @@
+rcpplint:
+	3rdparty/dmlc-core/scripts/lint.py mxnet-rcpp ${LINT_LANG} R-package/src
+
+rpkg:
+	mkdir -p R-package/inst/libs
+	cp src/io/image_recordio.h R-package/src
+	if [ -d "lib" ]; then \
+		cp -rf lib/libmxnet.so R-package/inst/libs; \
+		if [ -e "lib/libtvm_runtime.so" ]; then \
+			cp -rf lib/libtvm_runtime.so R-package/inst/libs; \
+		fi; \
+	else \
+		cp -rf build/libmxnet.so R-package/inst/libs; \
+		if [ -e "build/libtvm_runtime.so" ]; then \
+			cp -rf build/libtvm_runtime.so R-package/inst/libs; \
+		fi; \
+	fi
+
+	mkdir -p R-package/inst/include
+	cp -rl include/* R-package/inst/include
+	Rscript -e "if(!require(devtools)){install.packages('devtools', repo = 'https://cloud.r-project.org/')}"
+	Rscript -e "if(!require(roxygen2)||packageVersion('roxygen2') < '6.1.1'){install.packages('roxygen2', repo = 'https://cloud.r-project.org/')}"
+	Rscript -e "library(devtools); library(methods); options(repos=c(CRAN='https://cloud.r-project.org/')); install_deps(pkg='R-package', dependencies = TRUE)"
+	cp R-package/dummy.NAMESPACE R-package/NAMESPACE  # NAMESPACE will be replaced by devtools::document later
+	echo "import(Rcpp)" >> R-package/NAMESPACE
+	R CMD INSTALL R-package
+	Rscript -e "require(mxnet); mxnet:::mxnet.export('R-package'); warnings()"
+	Rscript -e "devtools::document('R-package');warnings()"
+	R CMD INSTALL R-package
+
+rpkgtest:
+	Rscript -e 'require(testthat);res<-test_dir("R-package/tests/testthat");if(!testthat:::all_passed(res)){stop("Test failures", call. = FALSE)}'
+	Rscript -e 'res<-covr:::package_coverage("R-package");fileConn<-file(paste("r-package_coverage_",toString(runif(1)),".json"));writeLines(covr:::to_codecov(res), fileConn);close(fileConn)'
diff --git a/R-package/R/callback.R b/R-package/R/callback.R
@@ -16,6 +16,7 @@
 # under the License.
 
 #' @export mx.metric.logger
+library(methods)
 mx.metric.logger <- setRefClass("mx.metric.logger", fields = list(train = "numeric", eval="numeric"))
 
 #' Log training metric each period

diff --git a/R-package/R/zzz.R b/R-package/R/zzz.R
@@ -34,8 +34,18 @@ NULL
 .onLoad <- function(libname, pkgname) {
   # Require methods for older versions of R
   require(methods)
-  tryCatch(library.dynam("libmxnet", pkgname, libname, local=FALSE), error = function(e) { print('Loading local: inst/libs/libmxnet.so'); dyn.load("R-package/inst/libs/libmxnet.so", local=FALSE) })
-  tryCatch(library.dynam("mxnet", pkgname, libname), error = function(e) { print('Loading local: src/mxnet.so'); dyn.load("R-package/src/mxnet.so") })
+  tryCatch(library.dynam("libmxnet", pkgname, libname, local=FALSE), error = function(e) {
+    print('Loading libmxnet.so failed. Error:')
+    print(e)
+    print('Falling back to loading local: inst/libs/libmxnet.so')
+    dyn.load("R-package/inst/libs/libmxnet.so", local=FALSE)
+  })
+  tryCatch(library.dynam("mxnet", pkgname, libname), error = function(e) {
+    print('Loading mxnet.so failed. Error:')
+    print(e)
+    print('Falling back to loading local: src/mxnet.so')
+    dyn.load("R-package/src/mxnet.so")
+  })
   loadModule("mxnet", TRUE)
   init.symbol.methods()
   init.context.default()

diff --git a/R-package/src/Makevars b/R-package/src/Makevars
@@ -1,3 +1,4 @@
 CXX_STD = CXX11
-PKG_CPPFLAGS = -I../inst/include
-PKG_LIBS =  $(LAPACK_LIBS) $(BLAS_LIBS)
+PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) `pkg-config --libs opencv`
+PKG_CFLAGS = `pkg-config --cflags opencv`
+PKG_CPPFLAGS = -I../inst/include `pkg-config --cflags opencv` `Rscript -e 'Rcpp:::CxxFlags()'`
diff --git a/R-package/src/Makevars.win b/R-package/src/Makevars.win
@@ -1,3 +1,2 @@
-
 PKG_CPPFLAGS = -I../inst/include
 PKG_LIBS =  $(LAPACK_LIBS) $(BLAS_LIBS) -L../inst/libs/x64/ -llibmxnet
diff --git a/ci/docker/runtime_functions.sh b/ci/docker/runtime_functions.sh
@@ -1223,12 +1223,11 @@ unittest_ubuntu_cpu_R() {
     build_ccache_wrappers
     echo  "MAKEFLAGS = -j"$(nproc) > ~/.R/Makevars
     # make -j not supported
-    make rpkg                           \
-        USE_BLAS=openblas               \
+    make -f R-package/Makefile rpkg \
         R_LIBS=/tmp/r-site-library
 
     R CMD INSTALL --library=/tmp/r-site-library R-package
-    make rpkgtest R_LIBS=/tmp/r-site-library
+    make -f R-package/Makefile rpkgtest R_LIBS=/tmp/r-site-library
 }
 
 unittest_ubuntu_minimal_R() {
@@ -1239,8 +1238,7 @@ unittest_ubuntu_minimal_R() {
     build_ccache_wrappers
     echo  "MAKEFLAGS = -j"$(nproc) > ~/.R/Makevars
     # make -j not supported
-    make rpkg                           \
-        USE_BLAS=openblas               \
+    make -f R-package/Makefile rpkg \
         R_LIBS=/tmp/r-site-library
 
     R CMD INSTALL --library=/tmp/r-site-library R-package
@@ -1269,11 +1267,10 @@ unittest_ubuntu_gpu_R() {
     build_ccache_wrappers
     echo  "MAKEFLAGS = -j"$(nproc) > ~/.R/Makevars
     # make -j not supported
-    make rpkg                           \
-        USE_BLAS=openblas               \
+    make -f R-package/Makefile rpkg \
         R_LIBS=/tmp/r-site-library
     R CMD INSTALL --library=/tmp/r-site-library R-package
-    make rpkgtest R_LIBS=/tmp/r-site-library R_GPU_ENABLE=1
+    make -f R-package/Makefile rpkgtest R_LIBS=/tmp/r-site-library R_GPU_ENABLE=1
 }
 
 unittest_ubuntu_cpu_julia() {

diff --git a/docs/static_site/src/_includes/get_started/linux/r/cpu.md b/docs/static_site/src/_includes/get_started/linux/r/cpu.md
@@ -5,5 +5,6 @@ After you have setup R v3.4.4+ and MXNet, you can build and install the MXNet R
 
 {% highlight bash %}
 $ cd incubator-mxnet
-$ make rpkg
-{% endhighlight %}
+$ mkdir build; cd build; cmake -DUSE_CUDA=OFF ..; make -j $(nproc); cd ..
+$ make -f R-package/Makefile rpkg
+{% endhighlight %}
diff --git a/docs/static_site/src/_includes/get_started/linux/r/gpu.md b/docs/static_site/src/_includes/get_started/linux/r/gpu.md
@@ -10,7 +10,8 @@ MXNet as follows:
 
 {% highlight bash %}
 $ cd incubator-mxnet
-$ make rpkg
+$ mkdir build; cd build; cmake ..; make -j $(nproc); cd ..
+$ make -f R-package/Makefile rpkg
 {% endhighlight %}
 
-{% include /get_started/gpu_snippet.md %}
+{% include /get_started/gpu_snippet.md %}
diff --git a/docs/static_site/src/pages/get_started/osx_setup.md b/docs/static_site/src/pages/get_started/osx_setup.md
@@ -202,7 +202,7 @@ Run the following commands to install the MXNet dependencies and build the MXNet
     cd R-package
     Rscript -e "library(devtools); library(methods); options(repos=c(CRAN='https://cran.rstudio.com')); install_deps(dependencies = TRUE)"
     cd ..
-    make rpkg
+    make -f R-package/Makefile rpkg
 ```
 
 ## Install the MXNet Package for Julia

diff --git a/docs/static_site/src/pages/get_started/ubuntu_setup.md b/docs/static_site/src/pages/get_started/ubuntu_setup.md
@@ -363,23 +363,9 @@ make install
 
 ### Install the MXNet Package for R
 
-Building *MXNet* from source is a 2 step process.
-1. Build the *MXNet* core shared library, `libmxnet.so`, from source.
-2. Build the R bindings.
-
-#### Quick MXNet-R Installation
-You can quickly build MXNet-R with the following two scripts found in the `/docs/install` folder:
-
-```bash
-git clone --recursive https://github.com/apache/incubator-mxnet.git mxnet
-cd mxnet/docs/install
-./install_mxnet_ubuntu_python.sh
-./install_mxnet_ubuntu_r.sh
-```
-
-Or you can go through a manual process described next.
-
-#### Manual MXNet-R Installation
+Before you build MXNet for R from source code, you must complete
+[building the shared library](#build-the-shared-library).
+source root directory to build the MXNet Perl package:
 
 **Minimum Requirements**
 1. [GCC 4.8](https://gcc.gnu.org/gcc-4.8/) or later to compile C++ 11.
@@ -389,60 +375,43 @@ Or you can go through a manual process described next.
 
 **Build the MXNet core shared library**
 
-**Step 1** Install build tools and git.
+**Step 1** Install R, cran-devtools and dependencies
+
+To install R and the devtools, run
 
 ```bash
 sudo apt-get update
-sudo apt-get install -y build-essential git
+sudo apt-get install -y r-base-core r-cran-devtools libcairo2-dev libxml2-dev
 ```
 
-**Step 2** Install OpenBLAS.
+`libxml2-dev` is required for the `roxygen2` dependency and `libcairo2-dev` is
+required for the suggested `imager` dependency.
 
-*MXNet* uses [BLAS](https://en.wikipedia.org/wiki/Basic_Linear_Algebra_Subprograms)
-and [LAPACK](https://en.wikipedia.org/wiki/LAPACK) libraries for accelerated numerical computations
-on CPU machine. There are several flavors of BLAS/LAPACK libraries - [OpenBLAS](https://www.openblas.net/),
-[ATLAS](http://math-atlas.sourceforge.net/) and [MKL](https://software.intel.com/en-us/intel-mkl). In this step we
-install OpenBLAS. You can choose to install ATLAS or MKL.
+To generate documentation, it is also required to install `roxygen2`.
 
 ```bash
-sudo apt-get install -y libopenblas-dev liblapack-dev
+R
+> install.packages("roxygen2")
+> Would you like to use a personal library instead?  (y/n) y
+> Would you like to create a personal library ... to install packages into?  (y/n) y
 ```
 
-**Step 3** Install OpenCV.
+Note: To successfully complete the next step, you need a personal R library. If
+you were able to run `install.packages("roxygen2")` above, you either had
+already, or you have successfully created a personal library just now.
 
-*MXNet* uses [OpenCV](https://opencv.org/) for efficient image loading and augmentation operations.
+**Step 2** Make and install the MXNet-R bindings.
 
 ```bash
-sudo apt-get install -y libopencv-dev
+make -f R-package/Makefile rpkg
 ```
 
-**Step 4** Download MXNet sources and build MXNet core shared library. You can clone the repository as described in the
-following code block, or you may try the [download links](download) for your desired MXNet version.
-
-```bash
-git clone --recursive https://github.com/apache/incubator-mxnet mxnet
-cd mxnet
-echo "USE_OPENCV = 1" >> ./config.mk
-echo "USE_BLAS = openblas" >> ./config.mk
-make -j $(nproc)
-```
-
-*Note* - USE_OPENCV and USE_BLAS are make file flags to set compilation options to use OpenCV and BLAS library. You can
-explore and use more compilation options in `make/config.mk`.
-
-<br/>
-
-**Step 5** Make and install the MXNet-R bindings.
-
-```bash
-make rpkg
-```
 #### Verify MXNet-R Installation
 
 You can verify your MXNet-R installation as follows:
 
 ```bash
-sudo -i R
+R
 ```
 
 At the R prompt enter the following:

diff --git a/setup-utils/install-mxnet-ubuntu-r.sh b/setup-utils/install-mxnet-ubuntu-r.sh
@@ -59,7 +59,7 @@ sudo Rscript -e "library(devtools); library(methods); options(repos=c(CRAN='http
 cd ..
 
 echo "Compiling R package. This can take few minutes..."
-sudo make rpkg
+sudo make -f R-package/Makefile rpkg
 
 echo "Installing R package..."
 sudo R CMD INSTALL mxnet_current_r.tar.gz