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I can not compile R packages (like xlsx) which depend on rJava (another R package). Some weeks ago I had no problems.
If I try to compile rJava inside of R I get:
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 : '/usr/lib/jvm/java-7-openjdk/jre/bin/java'
archiver : '/usr/lib/jvm/java-7-openjdk/bin/jar'
compiler : '/usr/lib/jvm/java-7-openjdk/bin/javac'
header prep.: '/usr/lib/jvm/java-7-openjdk/bin/javah'
cpp flags : '-I/usr/lib/jvm/java-7-openjdk/include -I/usr/lib/jvm/java-7-openjdk/include/linux'
java libs : '-L/usr/lib/jvm/java-7-openjdk/jre/lib/amd64/server -ljvm'
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’
Any idea?
Last edited by rogorido (2014-09-08 16:10:15)
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I answer myself. The problem is not only archlinux-related[1]. A solution (or workaround) is to write
unset JAVA_HOME
before starting R. Then you can compile rJava.
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