报错信息

checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details.

Make sure you have Java Development Kit installed and correctly registered in R.

using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-qoPWdk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c conftest.c -o conftest.o
conftest.c:1:10: fatal error: jni.h: No such file or directory
1 | #include <jni.h>
|          ^~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:191: conftest.o] Error 1
Unable to compile a JNI program

解决方案

首先重新安装jdk，例如Java11的jdk以Ubuntu/Debian为例是`openjdk-11-jdk`：

sudo apt-get install openjdk-11-jdk -y

然后重新配置R的Java环境：

R CMD javareconf

问题解决

root@Rstudio:~# R CMD javareconf

Java interpreter : /usr/lib/jvm/default-java/bin/java

Java version     : 11.0.19

Java home path   : /usr/lib/jvm/default-java

Java compiler    : /usr/lib/jvm/default-java/bin/javac

Java headers gen.: 

Java archive tool: /usr/lib/jvm/default-java/bin/jar

trying to compile and link a JNI program
detected JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-qoPWdk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c conftest.c -o conftest.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/lib/server -ljvm -L/usr/lib/R/lib -lR
JAVA_HOME        : /usr/lib/jvm/default-java
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /usr/lib/R
Done.