问题
I am having problems with R and rJava. I know that this is an old issue. I tried first R CMD javareconf and then I tried to install rJava from source but I got the following error:
> install.packages("rJava", type = "source")
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://ftp.cixug.es/CRAN/src/contrib/rJava_0.9-11.tar.gz'
Content type 'application/x-gzip' length 675188 bytes (659 KB)
==================================================
downloaded 659 KB
* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether clang supports static inline...
yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/bin/java'
archiver : '/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bin/jar'
compiler : '/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bin/javac'
header prep.: '/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bin/javah'
cpp flags : '-I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin'
java libs : '-L/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/server -ljvm'
checking whether Java run-time works... yes
checking whether -Xrs is supported... yes
checking whether -Xrs will be used... yes
checking whether JNI programs can be compiled... yes
checking whether JNI programs run... yes
checking JNI data types... ok
checking whether JRI should be compiled (autodetect)... yes
checking whether debugging output should be enabled... no
checking whether memory profiling is desired... no
checking whether threads support is requested... no
checking whether callbacks support is requested... no
checking whether JNI cache support is requested... no
checking whether headless init is enabled... yes
checking whether JRI is requested... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status: creating src/config.h
=== configuring in jri (/private/var/folders/tq/f5jbfqp97y52w_y7byn05_fw0000gn/T/Rtmp1XKGtU/R.INSTALL23f7fd05bfb/rJava/jri)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local' --cache-file=/dev/null --srcdir=.
checking build system type... x86_64-apple-darwin18.5.0
checking host system type... x86_64-apple-darwin18.5.0
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking Java version... 1.8.0_144
checking Java compatibility version (integer)... 8
checking whether /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bin/javah actually works... yes
checking for target flags... -target 1.4 -source 1.4
checking whether Java interpreter works... checking whether JNI programs can be compiled... yes
checking whether JNI programs can be run... yes
checking JNI data types... ok
checking whether Rinterface.h exports R_CStackXXX variables... yes
checking whether Rinterface.h exports R_SignalHandlers... yes
configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating Makefile
config.status: creating run
config.status: creating src/config.h
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Rglue.c -o Rglue.o
Rglue.c:860:13: warning: unused function 'new_jrectRef' [-Wunused-function]
static SEXP new_jrectRef(JNIEnv *env, jobject a, const char *sig, SEXP dim ) {
^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c arrayc.c -o arrayc.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c callJNI.c -o callJNI.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c callback.c -o callback.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c fields.c -o fields.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c jri_glue.c -o jri_glue.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c loader.c -o loader.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c otables.c -o otables.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c rJava.c -o rJava.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c tools.c -o tools.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rJava.so Rglue.o arrayc.o callJNI.o callback.o fields.o init.o jri_glue.o loader.o otables.o rJava.o tools.o -L/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
(cd ../jri && make)
make -C src JRI.jar
/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bin/javac -target 1.4 -source 1.4 -d . ../Mutex.java ../RBool.java ../RConsoleOutputStream.java ../REXP.java ../RFactor.java ../RList.java ../RMainLoopCallbacks.java ../RVector.java ../Rengine.java ../package-info.java
warning: [options] bootstrap class path not set in conjunction with -source 1.4
warning: [options] source value 1.4 is obsolete and will be removed in a future release
warning: [options] target value 1.4 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
4 warnings
if [ -n "/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bin/javah" ]; then /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bin/javah -d . -classpath . org.rosuda.JRI.Rengine; fi
clang -c -o Rengine.o Rengine.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -Wall -g -O2 -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -fno-common -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include
clang -c -o jri.o jri.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -Wall -g -O2 -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -fno-common -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include
clang -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -Wall -g -O2 -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -fno-common -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include
clang -c -o Rinit.o Rinit.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -Wall -g -O2 -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -fno-common -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include
clang -c -o globals.o globals.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -Wall -g -O2 -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -fno-common -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin
clang -c -o rjava.o rjava.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -Wall -g -O2 -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin -fno-common -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/include/darwin
clang -o libjri.jnilib Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o -dynamiclib -framework JavaVM -fopenmp -L/usr/local/lib -F/Library/Frameworks/R.framework/.. -framework R -lpcre -llzma -lbz2 -lz -licucore -ldl -lm -liconv
clang: error: unsupported option '-fopenmp'
make[2]: *** [libjri.jnilib] Error 1
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava’
The downloaded source packages are in
‘/private/var/folders/tq/f5jbfqp97y52w_y7byn05_fw0000gn/T/RtmpOubVUD/downloaded_packages’
Warning message:
In install.packages("rJava", type = "source") :
installation of package ‘rJava’ had non-zero exit status
回答1:
on High Sierra (10.13) , installing llvm as neilfws said, worked. macos has version 10 of clang, and installing llvm from brew set up version 9, which worked.
Note and follow the comments from brew about the install being 'keg only' and that you have to modify PATH, LDLIBs etc to point everything to the brew version.
来源：https://stackoverflow.com/questions/55997439/error-when-trying-to-install-rjava-from-source-on-macos-mojave