我正在尝试在rJava上的R上安装Mac High Sierra 10.13.6软件包。
install.packages("rJava")
工作正常，但是当我尝试加载软件包时，我得到了：
Error: package or namespace load failed for ‘rJava’:
.onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home/lib/server/libjvm.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
Reason: no suitable image found. Did find:
/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries/libjvm.dylib: mach-o, but wrong architecture
/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries/libclient.dylib: mach-o, but wrong architecture
我尝试通过以下方法来关注this：
install.packages('rJava', repos = 'http://rforge.net')
但是收到此错误消息：
configure: error: One or more Java configuration variables are not set.
Make sure R is configured with full Java support (including JDK). Run
R CMD javareconf
as root to add Java support to R.
If you don't have root privileges, run
R CMD javareconf -e
to set all Java-related variables and then install rJava.
ERROR: configuration failed for package ‘rJava’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
因此尝试运行：
sudo R CMD javareconf
但是我得到了：
detected JNI linker flags : -L/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries -ljvm
/usr/local/clang4/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c conftest.c -o conftest.o
conftest.c:1:10: fatal error: 'jni.h' file not found
#include <jni.h>
^~~~~~~
1 error generated.
make: *** [conftest.o] Error 1
Unable to compile a JNI program
因此尝试使用以下方法将R与java重新安装：
brew reinstall R --with-openblas --with-java
但是我收到此错误消息：
checking whether mixed C/Fortran code can be run... configure: WARNING: cannot run mixed C/Fortran code
configure: error: Maybe check LDFLAGS for paths to Fortran libraries?
我的gfortran是从here abd下载的，位于：
/usr/local/gfortran
所以我设置：
export LDFLAGS="-L/usr/local/gfortran/lib -lgfortran"
$ echo $LDFLAGS
-L/usr/local/gfortran/lib -lgfortran
$ ls /usr/local/gfortran/lib
gcc libatomic.la libgcc_ext.10.4.dylib libgfortran.spec libitm.la libquadmath.la libstdc++.a libubsan.dylib
i386 libcc1.0.so libgcc_ext.10.5.dylib libgomp.1.dylib libitm.spec libsanitizer.spec libstdc++.a-gdb.py libubsan.la
libasan.3.dylib libcc1.la libgcc_s.1.dylib libgomp.a libobjc-gnu.4.dylib libssp.0.dylib libstdc++.dylib
libasan.dylib libcc1.so libgcc_s_ppc64.1.dylib libgomp.dylib libobjc-gnu.a libssp.a libstdc++.la
libasan.la libcilkrts.5.dylib libgcc_s_x86_64.1.dylib libgomp.la libobjc-gnu.dylib libssp.dylib libstdc++fs.a
libasan_preinit.o libcilkrts.a libgfortran.3.dylib libgomp.spec libobjc-gnu.la libssp.la libstdc++fs.la
libatomic.1.dylib libcilkrts.dylib libgfortran.a libitm.1.dylib libquadmath.0.dylib libssp_nonshared.a libsupc++.a
libatomic.a libcilkrts.la libgfortran.dylib libitm.a libquadmath.a libssp_nonshared.la libsupc++.la
libatomic.dylib libcilkrts.spec libgfortran.la libitm.dylib libquadmath.dylib libstdc++.6.dylib libubsan.0.dylib
我重新跑了：
R --with-openblas --with-java
但是它会产生相同的错误。
我看到的是它一直在打印：
checking for Fortran 77 libraries of gfortran... -L/usr/local/opt/openblas/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0 -L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/gcc/x86_64-apple-darwin17.7.0/8.2.0/../../.. -lgfortran -lquadmath -lm
其中不包括我添加到LDFLAGS的路径。
所以我的问题是：
rJava在R上工作？R --with-openblas --with-java成功完成开始。