rj package compilation failure

Question

Thanks a lot for taking a look. There's a previous post on here with the same error message "cannot compile a simple JNI program" and the solution was to update to R 1.15. But I've already had everything in the newest version. Although it says "see config.log for details", it doesn't give a location, and "find / -name config.log" at the terminal returns nothing.

It's be an exhausting and frustrating process trying to get this to work. Any help will be much appreciated.

R version 2.15.1, 64-bit (I used Homebrew install, but it shouldn't be the problem)

Eclipse 4.2 Cocoa, 64-bit (tried 3.7 as well, didn't work either)

OSX 10.7.5

Here's the error message:

install.packages(c("rj"), repos="http://download.walware.de/rj-1.1")
Installing package(s) into '/Library/Frameworks/R.framework/Versions/2.15/Resources/library'
(as 'lib' is unspecified)
trying URL 'http://download.walware.de/rj-1.1/src/contrib/rj_1.1.0-4.tar.gz'
Content type 'application/x-tar' length 314501 bytes (307 Kb)
opened URL
==================================================
downloaded 307 Kb

* installing *source* package 'rj' ...
checking R config... found
    R_HOME   : /usr/local/Cellar/r/2.15.1/R.framework/Resources
checking for gcc... cc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking Java support in R... ok
    JAVA_HOME: /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
    JAVA     : /usr/bin/java
    JAVAC    : /usr/bin/javac
    JAVAH    : /usr/bin/javah
    JAVA_CPPFLAGS: -I/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/include
    JAVA_LIBS: -framework JavaVM
    JAR      : /usr/bin/jar

configure: creating ./config.status
config.status: creating src/Makevars
=== configuring in jri (/private/var/folders/7p/q7qb1n2d277c9tqt65s5wy_c0000gn/T/RtmpVlP2YK/R.INSTALL2c9175fac4e/rj/jri)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local'  --cache-file=/dev/null --srcdir=.
checking build system type... i386-apple-darwin11.4.2
checking host system type... i386-apple-darwin11.4.2
checking for gcc... cc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking how to run the C preprocessor... cc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking whether Java interpreter works... checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details.
configure: error: ./configure failed for jri
ERROR: configuration failed for package 'rj'
* removing '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rj'
* restoring previous '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rj'

The downloaded source packages are in
    '/private/var/folders/7p/q7qb1n2d277c9tqt65s5wy_c0000gn/T/RtmpNM4Pyx/downloaded_packages'
Warning message:
In install.packages(c("rj"), repos = "http://download.walware.de/rj-1.1") :
  installation of package 'rj' had non-zero exit status

Here is the session info.

sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin11.4.0 (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tcltk_2.15.1 tools_2.15.1

For those able to help (that won't be me) it might be useful for you to explain why what you've attempted here doesn't seem to match the installation instructions. — joran
I don't understand what you mean. The instruction says install.packages(c("rj", "rj.gd"), repos="download.walware.de/rj-1.1"). I'm just installing the first package and not both at the same time. If it helps anyone to know: using the exact command on my machine produces the same error for the other package as well. — Centzon Totochtin
That was all I meant (I wasn't sure whether installing both made a difference or not). — joran
Ah I was hoping you spotted something that might be the cause of the error. Thanks for bringing it up nonetheless. — Centzon Totochtin

ravi sundriyal ravi sundriyal · Accepted Answer · 2016-07-10T02:23:15

I faced the same issue and below Solution worked for me. Please follow the steps

1.) You need to run this command on the terminal - R CMD javareconf 2.) After that check the compatibility of StatET with rJ package which is in below order.

For RJ 2.0 (StatET 3.4 - 3.5): install.packages(c("rj", "rj.gd"), repos="http://download.walware.de/rj-2.0")

For RJ 1.1 (StatET 3.0 - 3.3): install.packages(c("rj", "rj.gd"), repos="http://download.walware.de/rj-1.1")

For RJ 1.0 (StatET 2.0): install.packages(c("rj", "rj.gd"), repos="http://download.walware.de/rj-1.0")

For RJ 0.5 (StatET 0.10): install.packages("rj", repos="http://download.walware.de/rj-0.5")

3.) Once you know your compatible version in accordance with StatET then run the package installation command. for example. I am using a StatET 3.5 thus for me RJ 2.0 will work and not others .

So command would be {install.packages(c("rj", "rj.gd"), repos="http://download.walware.de/rj-2.0")}

4.) Once your installation is done then do check the environmental variable are set correctly in case you are using any IDE ( Like Eclipse ). Library paths should be set in Eclipse or any other IDE.

Follow this link in case of any issues - http://www.walware.de/?page=/it/statet/installation.html

rj package compilation failure

1 Answers