Closed akhst7 closed 2 years ago
egeulgen
commented
2 years ago hey @akhst7,
It seems that most likely R cannot find the JAVA_HOME env variable. Try running R CMD javareconf in the terminal, then installing R . If that doesn't resolve the issue, please share the output of Sys.getenv("JAVA_HOME")
akhst7
commented
2 years ago @egeulgen, after a bit of struggle and investigation, I found there was another java installed by Homebrew. I got rid of it, reinstalled Oracle openJDK 17, set JAVA_HOME, and run R CMD javareconf. And pathfindR was installed without a hitch.
Thanks.
R CMD javareconf 08:11:14 PM
Java interpreter : /Library/Java/JavaVirtualMachines/jdk-17.0.1.jdk/Contents/Home/bin/java
Java version : 17.0.1
Java home path : /Library/Java/JavaVirtualMachines/jdk-17.0.1.jdk/Contents/Home
Java compiler : /Library/Java/JavaVirtualMachines/jdk-17.0.1.jdk/Contents/Home/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /Library/Java/JavaVirtualMachines/jdk-17.0.1.jdk/Contents/Home/bin/jar
trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/darwin
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
/opt/homebrew/opt/llvm/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk-17.0.1.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-17.0.1.jdk/Contents/Home/include/darwin -I"/opt/homebrew/Cellar/hdf5/1.12.1/include" -I"/opt/homebrew/opt/szip/include" -I"/opt/homebrew/opt/gettext/include" -I"/opt/homebrew/opt/llvm/include" -I"/opt/homebrew/opt/libomp/include" -isysroot "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk" -Xclang -fopenmp -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c conftest.c -o conftest.o
/opt/homebrew/opt/llvm/bin/clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/homebrew/opt/llvm/lib -L/opt/homebrew/opt/bison/lib -L/opt/homebrew/opt/gettext/lib -Wl,-rpath,/opt/homebrew/opt/llvm/lib --sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -lomp -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk-17.0.1.jdk/Contents/Home/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk-17.0.1.jdk/Contents/Home
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/darwin
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.R_LDPATH was also set right;
/Library/Frameworks/R.framework/Resources/etc ❯ more ldpaths 08:22:03 PM
: ${JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-17.0.1.jdk/Contents/Home}
: ${R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/server}
if test -n ""; then
: ${R_LD_LIBRARY_PATH=${R_HOME}/lib:}
else
: ${R_LD_LIBRARY_PATH=${R_HOME}/lib}
fi
if test -n "${R_JAVA_LD_LIBRARY_PATH}"; then
R_LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${R_JAVA_LD_LIBRARY_PATH}"
fi
## This is DYLD_FALLBACK_LIBRARY_PATH on Darwin (macOS) and
## LD_LIBRARY_PATH elsewhere.
## However, on macOS >=10.11 (if SIP is enabled, the default), the
## environment value will not be passed to a script such as R.sh, so
## would not seen here.
if test -z "${DYLD_FALLBACK_LIBRARY_PATH}"; then
DYLD_FALLBACK_LIBRARY_PATH="${R_LD_LIBRARY_PATH}"
else
DYLD_FALLBACK_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${DYLD_FALLBACK_LIBRARY_PATH}"
fi
export DYLD_FALLBACK_LIBRARY_PATH
Hi,
pathfindR failed to be built with a following error;
OpenJDK is installed;
It looks like the install script fails to see the location of openJDK ?
Here is a set up for my Mimi;