Comments (10)
kevinushey
commented on June 11, 2024
1
Normally, /usr/local/include should show up after RcppArmadillo's headers, so I suspect this is a local configuration issue on your side. When I compile RcppArmadillo, I see:
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/kevin/Library/R/3.4/library/Rcpp/include" -I/usr/local/include -I../inst/include -fPIC -Wall -g -O2 -c RcppArmadillo.cpp -o RcppArmadillo.o
Note that -I/usr/local/include comes after Rcpp in this case. See also:
kevin@cdrv:~/r
$ R CMD config --all
CC = clang
CFLAGS = -g -O3 -Wall -pedantic -mtune=native -I/usr/local/opt/openssl/include
CPICFLAGS = -fPIC
CPP = clang -E
CPPFLAGS = -I/usr/local/include
CXX = clang++
CXXCPP = clang++ -E
CXXFLAGS = -g -O3 -Wall -pedantic -mtune=native -Wno-unused-local-typedef -I/usr/local/opt/openssl/include
CXXPICFLAGS = -fPIC
CXX11 = clang++
CXX11STD = -std=gnu++11
CXX11FLAGS = -Wall -g -O2
CXX11PICFLAGS = -fPIC
CXX14 = clang++
CXX14STD = -std=gnu++14
CXX14FLAGS = -Wall -g -O2
CXX14PICFLAGS = -fPIC
CXX98 = clang++
CXX98STD =
CXX98FLAGS = -Wall -g -O2
CXX98PICFLAGS = -fPIC
CXX17 = clang++
CXX17STD = -std=gnu++1z
CXX17FLAGS = -Wall -g -O2
CXX17PICFLAGS = -fPIC
CXX1X = clang++ -std=c++11
CXX1XSTD = -std=c++11
CXX1XFLAGS = -g -O3 -Wall -pedantic -mtune=native -Wno-unused-local-typedef -I/usr/local/opt/openssl/include
CXX1XPICFLAGS = -fPIC
DYLIB_EXT = .dylib
DYLIB_LD = clang
DYLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -fopenmp
F77 = gfortran
FFLAGS = -g -O3 -mtune=native
FPICFLAGS = -fPIC
FLIBS = -L/usr/local/Cellar/gcc/6.3.0_1/lib/gcc/6
SAFE_FFLAGS = -g -O2 -ffloat-store
FC = gfortran
FCFLAGS = -g -O3 -mtune=native
FCPICFLAGS = -fPIC
OBJC = clang
OBJCFLAGS = -Wall -g -O2 -fobjc-exceptions
JAVA = /usr/bin/java
JAVAC = /usr/bin/javac
JAVAH = /usr/bin/javah
JAR = /usr/bin/jar
JAVA_HOME = /Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk/Contents/Home/jre
JAVA_LIBS = -L/Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk/Contents/Home/jre/lib/server -ljvm
JAVA_CPPFLAGS = -I/Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk/Contents/Home/jre/../include/darwin
LDFLAGS = -L/usr/local/opt/openssl/lib
SHLIB_CFLAGS =
SHLIB_CXXLD = clang++
SHLIB_CXXLDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
SHLIB_CXX98LD = clang++
SHLIB_CXX98LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
SHLIB_CXX11LD = clang++ -std=gnu++11
SHLIB_CXX11LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
SHLIB_CXX14LD = clang++ -std=gnu++14
SHLIB_CXX14LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
SHLIB_CXX17LD = clang++ -std=gnu++1z
SHLIB_CXX17LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
SHLIB_EXT = .so
SHLIB_FFLAGS =
SHLIB_LD = clang
SHLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
SHLIB_FCLD = gfortran
SHLIB_FCLDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
SHLIB_CXX1XLD = clang++ -std=gnu++11
SHLIB_CXX1XLDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
TCLTK_CPPFLAGS = -I/usr/local/include -I/usr/local/include -I/opt/X11/include
TCLTK_LIBS = -L/usr/local/lib -ltcl8.6 -L/usr/local/lib -ltk8.6 -L/opt/X11/lib -lX11 -Wl,-weak-lXss -lXext
BLAS_LIBS = -L/Library/Frameworks/R.framework/Resources/lib -lRblas
LAPACK_LIBS = -L/Library/Frameworks/R.framework/Resources/lib -lRlapack
MAKE = make
LIBnn = lib
LOCAL_SOFT =
COMPILED_BY =
I suspect you have some local configuration that's placing /usr/local/include earlier during compilation.
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coatless
commented on June 11, 2024
1
FYI: You can directly download and use the official gfortran binaries now if you are on R 3.4.
FAQ guidance is being updated.
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eddelbuettel
commented on June 11, 2024
Well, I have been building RcppArmadillo for all those years, and most of the time I have Armadillo also as a system library from the OS (mostly Ubuntu) and never had issues. Neither had the folks building eg MLPACK and RcppMLPACK. So I think this ought to be configurable at your end.
But I defer to the macOS users for details: @coatless @thirdwing @kevinushey -- can you help?
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kevinushey
commented on June 11, 2024
I haven't seen this issue before on macOS with RcppArmadillo. I saw one mailing list post on this here:
http://lists.r-forge.r-project.org/pipermail/rcpp-devel/2014-November/008184.html
but it looks like the user was only seeing this issue when using a version of R built from sources themselves -- but then I haven't seen that with my own builds either.
Are you using CRAN R, or something else?
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notcome
commented on June 11, 2024
I download R to get core R binaries and use R Studio to install R packages. Not an expert on R.
Nonetheless, the compiler options by Rcpp listed in the log shows:
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include" -fPIC -Wall -mtune=core2 -g -O2 -c
which does put /usr/local/include before RcppArmadillo’s own headers. A conflict is thus an expected behavior.
Added: And I did put the headers for system-wide Armadillo in /usr/local/include.
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notcome
commented on June 11, 2024
My point is that since RcppArmadillo comes with its own Armadillo binaries and headers, during compilation that version should be used over a system-wide one. The problem can certainly be overcome by my end, by disabling ARMA_USE_WRAPPER on the system version and explicitly link my program with BLAS (on macOS, it is Accelerate framework). It just appears to be a hacky solution to a dependency issue.
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eddelbuettel
commented on June 11, 2024
But the included version is being used. Do R CMD INSTALL RcppArmdillo_*.tar.gz and look closely at the include flags. Also, RcppArmadillo does not link against any Armadillo library.
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kevinushey
commented on June 11, 2024
FWIW the other report I saw re: this sort of error occurred when R was built to use Accelerate (I normally use OpenBLAS when building from source) so it's entirely possible what you're seeing is somehow related to that (although it would be surprising)
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notcome
commented on June 11, 2024
Thanks for all the help! It seems that my R configuration is totally corrupted to the point that I cannot even “R CMD config --all”. I just re-installed my R. I do not even know why (completely new at R, helping others writing C++ code) (maybe R Studio?).
Thanks anyway! Sorry for disturbing.
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eddelbuettel
commented on June 11, 2024
The Rcpp FAQ has sections with pointers to detailed help for OS X / macOS installations.
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