update non-GPU Makevars

Author: jianxiaoyang

src/MakevarsCPU.in

@@ -0,0 +1,77 @@
+## Use the R_HOME indirection to support installations of multiple R version
+PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"`
+
+## As an alternative, one can also add this code in a file 'configure'
+##
+##    PKG_LIBS=`${R_HOME}/bin/Rscript -e "Rcpp:::LdFlags()"`
+##
+##    sed -e "s|@PKG_LIBS@|${PKG_LIBS}|" \
+##        src/Makevars.in > src/Makevars
+##
+## which together with the following file 'src/Makevars.in'
+##
+##    PKG_LIBS = @PKG_LIBS@
+##
+## can be used to create src/Makevars dynamically. This scheme is more
+## powerful and can be expanded to also check for and link with other
+## libraries.  It should be complemented by a file 'cleanup'
+##
+##    rm src/Makevars
+##
+## which removes the autogenerated file src/Makevars.
+##
+## Of course, autoconf can also be used to write configure files. This is
+## done by a number of packages, but recommended only for more advanced users
+## comfortable with autoconf and its related tools.
+
+PKG_CPPFLAGS = -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION
+PKG_CXXFLAGS = -g1
+
+OBJECTS.cyclops = \
+    cyclops/CcdInterface.o \
+    cyclops/CompressedDataMatrix.o \
+    cyclops/CyclicCoordinateDescent.o \
+    cyclops/ModelData.o \
+    cyclops/Timer.o
+
+OBJECTS.drivers = \
+    cyclops/drivers/AbstractCrossValidationDriver.o \
+    cyclops/drivers/AbstractDriver.o \
+    cyclops/drivers/AbstractSelector.o \
+    cyclops/drivers/AutoSearchCrossValidationDriver.o \
+    cyclops/drivers/BootstrapDriver.o \
+    cyclops/drivers/BootstrapSelector.o \
+    cyclops/drivers/CrossValidationSelector.o \
+    cyclops/drivers/WeightBasedSelector.o \
+    cyclops/drivers/GridSearchCrossValidationDriver.o \
+    cyclops/drivers/HierarchyAutoSearchCrossValidationDriver.o \
+    cyclops/drivers/HierarchyGridSearchCrossValidationDriver.o \
+    cyclops/drivers/ProportionSelector.o
+
+OBJECTS.priors = \
+    cyclops/priors/CovariatePrior.o
+
+OBJECTS.io = \
+    cyclops/io/InputReader.o
+
+OBJECTS.engine = \
+    cyclops/engine/AbstractModelSpecifics.o
+
+OBJECTS.utils = \
+    utils/HParSearch.o
+
+OBJECTS.thread = \
+    tinythread/tinythread.o
+
+OBJECTS.R = \
+    IsSorted.o \
+    RcppExports.o \
+    RcppModelData.o \
+    RcppCyclopsInterface.o \
+    RcppGpuInterface.o \
+    RcppIsSorted.o
+
+OBJECTS = $(OBJECTS.cyclops) $(OBJECTS.drivers) \
+          $(OBJECTS.engine) $(OBJECTS.utils) \
+          $(OBJECTS.threads) $(OBJECTS.R) \
+          $(OBJECTS.priors) $(OBJECTS.io)

tests/testthat/test-gpucox.R

@@ -3,13 +3,13 @@ library("testthat")
 library("survival")
 
 
-GpuDevice <- listOpenCLDevices()[1] # "TITAN V"
-# GpuDevice <- listOpenCLDevices()[2] # "GeForce RTX 2080"
+GpuDevice <- listOpenCLDevices()[1]
 tolerance <- 1E-4
 
 
 # small cox
 test_that("Check small Cox on GPU", {
+    skip_if(length(listOpenCLDevices()) == 0, "GPU not available")
     test <- read.table(header=T, sep = ",", text = "
                    start, length, event, x1, x2
                        0, 4,  1,0,0
@@ -34,6 +34,7 @@ test_that("Check small Cox on GPU", {
 })
 
 test_that("Check very small Cox example with time-ties", {
+    skip_if(length(listOpenCLDevices()) == 0, "GPU not available")
     test <- read.table(header=T, sep = ",", text = "
 start, length, event, x1, x2
                        0, 4,  1,0,0
@@ -59,6 +60,7 @@ start, length, event, x1, x2
 
 # large cox
 test_that("Check Cox on GPU", {
+    skip_if(length(listOpenCLDevices()) == 0, "GPU not available")
     set.seed(123)
     sim <- simulateCyclopsData(nstrata = 1,
                                nrows = 100000,
@@ -83,6 +85,7 @@ test_that("Check Cox on GPU", {
 
 # lasso cv
 test_that("Check cross-validation for lasso Cox on GPU", {
+    skip_if(length(listOpenCLDevices()) == 0, "GPU not available")
     set.seed(123)
     sim <- simulateCyclopsData(nstrata = 1,
                                nrows = 900,
@@ -112,6 +115,7 @@ test_that("Check cross-validation for lasso Cox on GPU", {
 
 # multi-core
 test_that("Check multi-core cross-validation for lasso Cox on GPU", {
+    skip_if(length(listOpenCLDevices()) == 0, "GPU not available")
     set.seed(123)
     sim <- simulateCyclopsData(nstrata = 1,
                                nrows = 900,

tests/testthat/test-timevaryingCox.R

@@ -5,6 +5,7 @@ GpuDevice <- listOpenCLDevices()[1]
 tolerance <- 1E-4
 
 test_that("Check very small Cox example with time-varying coefficient as stratified model", {
+    skip_if(length(listOpenCLDevices()) == 0, "GPU not available")
     test <- read.table(header=T, sep = ",", text = "
             start, length, event, x1, x2
             0, 4,  1,0,0