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Fail to install rJava Centos 6.3 #20

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orzZXY opened this issue Jul 18, 2014 · 2 comments
Closed

Fail to install rJava Centos 6.3 #20

orzZXY opened this issue Jul 18, 2014 · 2 comments

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@orzZXY
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orzZXY commented Jul 18, 2014

I failed to install rJava in R 2.15.3, with Sun Java 1..6 and gcc 4.4.
I saw a similar problem in stack overflow, someone was having the exact same problem as me, and he was using ubuntu 12.04 with gcc 4.7. He solved the problem with updating his ubuntu to 12.10 with gcc 4.8
What shall I do ? Do I need to updata my gcc to 4.8?

Thank you so very much.

[root@szwg-bigpipe-rh-003.szwg01.baidu.com R]# bin/R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.6.0_26
Java home path   : /opt/jdk1.6.0_26/jre
Java compiler    : /usr/bin/javac
Java headers gen.: 
Java archive tool: /usr/bin/jar
NOTE: Your JVM has a bogus java.library.path system property!
      Trying a heuristic via sun.boot.library.path to find jvm library...

 ** WARNING: auto-detection could not find libjvm!
    Your JVM has likely invalid java.library.path property,
    you may want to fix the JVM or set JAVA_LD_LIBRARY_PATH manually.
Java library path: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm
JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux

Updating Java configuration in /opt/R
Done.
[root@s R]# bin/R CMD INSTALL library/ packages/rJava_0.9-3.tar.gz 
Warning: invalid package 'library/'
* installing to library '/opt/R/library'
* installing *source* package 'rJava' ...
** package 'rJava' successfully unpacked and MD5 sums checked
checking for gcc... /usr/bin/make64 MAC=64 -s -f /opt/R/etc/Makeconf -f /opt/R/share/make/config.mk print R_HOME=/opt/R VAR=CC
gcc -std=gnu99
checking for C compiler default output file name... 
configure: error: C compiler cannot create executables
See `config.log' for more details.
configure: WARNING: Cache variable ac_cv_prog_ac_ct_CC contains a newline.
ERROR: configuration failed for package 'rJava'
* removing '/opt/R/library/rJava'
@s-u
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s-u commented Jul 29, 2014

This seems more like a badly misconfigured system. On one hand it seems that you JDK is incomplete (see first part) and on the other hand it seems like your compiler (CC) settings are bogus (see the second part) - check R CMD config CC it seems that it's creating invalid output.

@orzZXY
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orzZXY commented Jul 30, 2014

Thank you very much. I changed to Ubuntu 12.04 and problem solved by using apt-get. You're right about the problem though, the system is designed for our company and it's lots of bugs. Thank you.

@orzZXY orzZXY closed this as completed Jul 30, 2014
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