在RHEL6上安装rJava:即使使用相同的Java路径，我也得到：错误：一个或多个JNI类型与相应的本机类型不同

Question

 conda-env version : 4.3.13
 conda-build version : 2.1.4
 python version : 2.7.13.final.0
 rpy2 : 2.8.5

我安装rpy2是为了在Python中使用R。但是在安装conda的R版本中，我在安装“rjava”时遇到了问题。

checking whether Java run-time works... yes
checking whether -Xrs is supported... yes
checking whether JNI programs can be compiled... yes
checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this.
ERROR: configuration failed for package 'rJava'

与我的独立版本的R安装在同一台机器上，我没有问题，所以我知道我有正确的版本安装。

对于我使用相同R版本的两个不同设置（独立R和R with conda），我有相同的Java版本

 java -version
openjdk version "1.8.0_121"
OpenJDK Runtime Environment (build 1.8.0_121-b13)
OpenJDK 64-Bit Server VM (build 25.121-b13, mixed mode)

对于这两个设置，以下变量都不退出

R_JAVA_LD_LIBRARY_PATH
JAVA_HOME

定义了。Standalone的路径非常相似：

PATH=/opt/ccda/anaconda2/bin:/opt/opennlp/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

PATH=/opt/ccda/anaconda2/envs/py27CCA/bin:/opt/ccda/anaconda2/bin:/opt/ccda/anaconda2/bin:/opt/opennlp/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

这里是编译期间的信息。对于独立的R版本：

interpreter : '/usr/bin/java'
archiver    : '/usr/bin/jar'
compiler    : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags   : '-I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include/linux'
java libs   : '-L/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/lib/amd64/server -ljvm

而对于与Conda一起安装的R版本：

interpreter : '/usr/lib/jvm/java/jre/bin/java'
archiver    : '/usr/lib/jvm/java/jre/../bin/jar'
compiler    : '/usr/lib/jvm/java/jre/../bin/javac'
header prep.: '/usr/lib/jvm/java/jre/../bin/javah'
cpp flags   : '-I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux'
java libs   : '-L/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/lib/amd64/server -ljvm'

我尝试使用以下方法获得相同的路径：

export JAVA_HOME=/usr/lib/jvm/jre-1.8.0-openjdk.x86_64/bin/java
export R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/amd64/server
export JAVA_CPPFLAGS="-I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include/linux"

/usr/bin/java -> /etc/alternatives/java
/etc/alternatives/java -> /usr/lib/jvm/jre-1.8.0-openjdk.x86_64/bin/java

 R CMD javareconf

interpreter : '/usr/bin/java'
archiver    : '/usr/bin/jar'
compiler    : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags   : '-I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include/linux'
java libs   : '-L/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/lib/amd64/server -ljvm'

R CMD javareconf
Java interpreter : /usr/lib/jvm/jre-1.8.0-openjdk.x86_64/bin/java
Java version     : 1.8.0_121
Java home path   : /usr/lib/jvm/jre-1.8.0-openjdk.x86_64
Java compiler    : /usr/lib/jvm/jre-1.8.0-openjdk.x86_64/../bin/javac
Java headers gen.: /usr/lib/jvm/jre-1.8.0-openjdk.x86_64/../bin/javah
Java archive tool: /usr/lib/jvm/jre-1.8.0-openjdk.x86_64/../bin/jar

trying to compile and link a JNI program
detected JNI cpp flags    : -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include/linux
detected JNI linker flags : -L/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/lib/amd64/server -ljvm
gcc -std=gnu99 -I/opt/ccda/anaconda2/envs/py27CCA/lib/R/include -DNDEBUG -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include/linux -I/opt/ccda/anaconda2/envs/py27CCA/include    -fpic  -I/opt/ccda/anaconda2/envs/py27CCA/include  -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/opt/ccda/anaconda2/envs/py27CCA/lib/R/lib -L/opt/ccda/anaconda2/envs/py27CCA/lib -lgfortran -o conftest.so conftest.o -L/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/lib/amd64/server -ljvm -L/opt/ccda/anaconda2/envs/py27CCA/lib/R/lib -lR


JAVA_HOME        : /usr/lib/jvm/jre-1.8.0-openjdk.x86_64
Java library path: /usr/lib/jvm/java/jre/lib/amd64/server
JNI cpp flags    : -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/../include/linux
JNI linker flags : -L/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.121-0.b13.el6_8.x86_64/jre/lib/amd64/server -ljvm
Updating Java configuration in /opt/ccda/anaconda2/envs/py27CCA/lib/R
Done.

我完全不明白错误信息的含义。我尝试了所有的建议，从不同的线程有关类似的问题。

编辑：使用导出

LD_LIBRARY_PATH=$JAVA_HOME/lib/amd64:$JAVA_HOME/lib/amd64/server 

解决了部分问题（在这种情况下不再需要JAVA_HOME)，但我还有其他问题：

/opt/ccda/anaconda2/envs/py27CCA/lib/libiconv.so
/opt/ccda/anaconda2/envs/py27CCA/lib/libiconv.so.2
/opt/ccda/anaconda2/envs/py27CCA/lib/libiconv.so.2.5.1
/opt/ccda/anaconda2/envs/py27CCA/lib/preloadable_libiconv.so

Answer 1

确保使用指向JDK的显式设置重新配置R环境。

确保JAVA_HOME指向JDK

export JAVA_HOME=your_JDK_installation

然后，重新配置R并显式传递所有位置

sudo R CMD javareconf \
JAVA_HOME=${JAVA_HOME} \
JAVA=${JAVA_HOME/bin/java \
JAVAC=${JAVA_HOME}/bin/javac \
JAVAH=${JAVA_HOME}/bin/javah \
JAR=${JAVA_HOME}/bin/jar \
JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/jre/lib/server \
JAVA_CPPFLAGS="-I${JAVA_HOME}/include -I${JAVA_HOME}/include/linux"

curl https://cran.r-project.org/src/contrib/rJava_0.9-8.tar.gz -o rJava_0.9-8.tar.gz
tar zxf rJava_0.9-8.tar.gz
cd rJava
./configure