Error Information:
[kupferd@rl01-int-p .R]$ R CMD INSTALL exactextractr_0.1.0.tar.gz
- installing to library ‘/home/kupferd/R/library’
- installing source package ‘exactextractr’ ...
** package ‘exactextractr’ successfully unpacked and MD5 sums checked
** using staged installation
configure: exactextractr: 0.1.0
checking for geos-config... /usr/bin/geos-config
checking geos-config usability... yes
configure: GEOS version: 3.5.0
checking geos version at least 3.6.0... no
Upgrade GEOS to version 3.6.0 or greater.
checking compiling and building against geos_c... yes
configure: PKG_CXX: g++
configure: PKG_CXXFLAGS: -O3 -std=c++11 -march=native -mtune=native -fPIC -I/usr/include
configure: PKG_LIBS: -Wl,-z,relro -L/usr/lib64 -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -L/opt/rh/devtoolset-7/root/usr/lib64 -I"/home/kupferd/R/library/Rcpp/include" -I/usr/local/include -O3 -std=c++11 -march=native -mtune=native -fPIC -I/usr/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -L/opt/rh/devtoolset-7/root/usr/lib64 -I"/home/kupferd/R/library/Rcpp/include" -I/usr/local/include -O3 -std=c++11 -march=native -mtune=native -fPIC -I/usr/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c exact_extract.cpp -o exact_extract.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -L/opt/rh/devtoolset-7/root/usr/lib64 -I"/home/kupferd/R/library/Rcpp/include" -I/usr/local/include -O3 -std=c++11 -march=native -mtune=native -fPIC -I/usr/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c exactextract/src/area.cpp -o exactextract/src/area.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -L/opt/rh/devtoolset-7/root/usr/lib64 -I"/home/kupferd/R/library/Rcpp/include" -I/usr/local/include -O3 -std=c++11 -march=native -mtune=native -fPIC -I/usr/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c exactextract/src/box.cpp -o exactextract/src/box.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -L/opt/rh/devtoolset-7/root/usr/lib64 -I"/home/kupferd/R/library/Rcpp/include" -I/usr/local/include -O3 -std=c++11 -march=native -mtune=native -fPIC -I/usr/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c exactextract/src/cell.cpp -o exactextract/src/cell.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -L/opt/rh/devtoolset-7/root/usr/lib64 -I"/home/kupferd/R/library/Rcpp/include" -I/usr/local/include -O3 -std=c++11 -march=native -mtune=native -fPIC -I/usr/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c exactextract/src/coordinate.cpp -o exactextract/src/coordinate.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -L/opt/rh/devtoolset-7/root/usr/lib64 -I"/home/kupferd/R/library/Rcpp/include" -I/usr/local/include -O3 -std=c++11 -march=native -mtune=native -fPIC -I/usr/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c exactextract/src/floodfill.cpp -o exactextract/src/floodfill.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -L/opt/rh/devtoolset-7/root/usr/lib64 -I"/home/kupferd/R/library/Rcpp/include" -I/usr/local/include -O3 -std=c++11 -march=native -mtune=native -fPIC -I/usr/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c exactextract/src/geos_utils.cpp -o exactextract/src/geos_utils.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -L/opt/rh/devtoolset-7/root/usr/lib64 -I"/home/kupferd/R/library/Rcpp/include" -I/usr/local/include -O3 -std=c++11 -march=native -mtune=native -fPIC -I/usr/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c exactextract/src/grid.cpp -o exactextract/src/grid.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -L/opt/rh/devtoolset-7/root/usr/lib64 -I"/home/kupferd/R/library/Rcpp/include" -I/usr/local/include -O3 -std=c++11 -march=native -mtune=native -fPIC -I/usr/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c exactextract/src/perimeter_distance.cpp -o exactextract/src/perimeter_distance.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -L/opt/rh/devtoolset-7/root/usr/lib64 -I"/home/kupferd/R/library/Rcpp/include" -I/usr/local/include -O3 -std=c++11 -march=native -mtune=native -fPIC -I/usr/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c exactextract/src/raster_cell_intersection.cpp -o exactextract/src/raster_cell_intersection.o
In file included from exactextract/src/floodfill.cpp:18:0:
exactextract/src/grid.h: In function ‘exactextract::Gridexactextract::bounded_extent exactextract::common_grid(T, T)’:
exactextract/src/grid.h:338:26: error: parameter declared ‘auto’
(auto& acc, auto& op) {
^
exactextract/src/grid.h:338:37: error: parameter declared ‘auto’
(auto& acc, auto& op) {
^
exactextract/src/raster_stats.h:214:68: note: candidate expects 0 arguments, 2 provided
make: *** [exact_extract.o] Error 1
ERROR: compilation failed for package ‘exactextractr’ - removing ‘/home/kupferd/R/library/exactextractr’
Description of issue -
Trying to install exactextractr package but I get an error which I think is related to the g++ version I am using or some compatibility issue. As far as I know the problem should be resolved by enabling c++11 compatibility, but that dit not work for me.
Steps taken so far -
I have tried different version of gcc and devtoolsets.
Here is my Makevars:
CXX14FLAGS=-O3 -std=c++11 -march=native -mtune=native -fPIC
#CXX14=/opt/rh/devtoolset-7/root/usr/bin/x86_64-redhat-linux-g++
CXX14=g++
MAKEFLAGS = -j8
System Information:
- RStudio Edition: (Server)
- RStudio Version: 1.1.383
- OS Version: Redhat 7.7
- R Version: 3.6
Also:
- Your
sessionInfo()
:
sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.7 (Maipo)
Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.0