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Problem: before upgrading, under Ubuntu14.04, I just installed the default JRE and JDK, and R 3.0.2 (the default for that rev of Ubuntu),and sucessfully ran R CMD javareconf.

However, since upgrading to 14.10, and verifying I have the latest java7 JRE and JDK, trying to run the javareconf fails with the following dump:

cellocgw@cellocgw-Studio-1747:~$ sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.7.0_65
Java home path   : /usr/lib/jvm/java-7-openjdk-amd64/jre
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar

trying to compile and link a JNI progam 
detected JNI cpp flags    : -I$(JAVA_HOME)/../include
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
In file included from conftest.c:1:0:
/usr/lib/jvm/java-7-openjdk-amd64/jre/../include/jni.h:39:19: fatal error: stdio.h: No such file or directory
 #include <stdio.h>
                   ^
compilation terminated.
/usr/lib/R/etc/Makeconf:133: recipe for target 'conftest.o' failed
make: *** [conftest.o] Error 1
Unable to compile a JNI program


JAVA_HOME        : /usr/lib/jvm/java-7-openjdk-amd64/jre
Java library path: 
JNI cpp flags    : 
JNI linker flags : 
Updating Java configuration in /usr/lib/R
Done.

Something is not installed or isn't where it "should" be. I've tried most of the tricks listed at similar questions (doing updates and the like), but so far I haven't found a question where the stdio.h file missing was the error message.

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  • If it's really looking for the <stdio.h> standard C library header, then that would require the libc6-dev package I think Dec 6, 2014 at 14:53
  • @steeldriver that sounds unlikely - I would have expected a stdio.h file right in the current ../include directory Dec 6, 2014 at 15:09
  • @steeldriver Looks like you were correct. See my answer; if you'd like to post a more precise answer I'll be happy to select your version. Dec 6, 2014 at 16:12

1 Answer 1

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I think I've solved this situation:

Based on a comment from steeldriver , I dug into the Software Center and added several "add-ons" to the gcc installation. I suspect that adding either libc6-dev or gcc-multilib was what I needed.

On a related note of probable interest to R users who want to install JGR : I had to install at least one of libpng12-dev, libpng3 , and libpng++dev to get the package png to install (in R), which is required for JGR to install.

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