[R] rjava on FreeBSD

Hasan Diwan hasan.diwan at gmail.com
Wed Jan 11 22:51:32 CET 2012 

Trying to install Rjava on FreeBSD 9 and am getting the following error:
> install.packages('rJava')
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-3.tar.gz'
Content type 'application/x-gzip' length 537153 bytes (524 Kb)
opened URL
==================================================
downloaded 524 Kb

* installing *source* package 'rJava' ...
** package 'rJava' successfully unpacked and MD5 sums checked
checking for gcc... gcc46 -std=gnu99
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 gcc46 -std=gnu99 accepts -g... yes
checking for gcc46 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc46 -std=gnu99 -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... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc46 -std=gnu99 supports static inline...
yes
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/local/bin/java'
archiver    : '/usr/local/bin/jar'
compiler    : '/usr/local/bin/javac'
header prep.: '/usr/local/bin/javah'
cpp flags   : '-I/usr/local/jdk1.6.0/jre/../include
-I/usr/local/jdk1.6.0/jre/../include/freebsd'
java libs   : '-L/usr/local/jdk1.6.0/jre/lib/i386/server
-L/usr/local/jdk1.6.0/jre/lib/i386
-L/usr/local/jdk1.6.0/jre/../lib/i386 -L -L/usr/java/packages/lib/i386
-L/lib -L/usr/lib -L/usr/local/lib -ljvm'
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'
* removing '/usr/local/lib/R/library/rJava'
* removing '/usr/local/lib/R/library/rJava'

The downloaded packages are in
        '/tmp/RtmpWtRfKe/downloaded_packages'
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages("rJava") :
  installation of package 'rJava' had non-zero exit status
2: In file.create(f.tg) :
  cannot create file '/usr/local/share/doc/R/html/packages.html',
reason 'Permission denied'
3: In make.packages.html(.Library) : cannot update HTML package index
>

Ok, so I tried doing so as root, because it would solve the
'Permissions denied' issue and was rewarded with:
> install.packages('rJava')
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-3.tar.gz'
Content type 'application/x-gzip' length 537153 bytes (524 Kb)
opened URL
==================================================
downloaded 524 Kb

* installing *source* package 'rJava' ...
** package 'rJava' successfully unpacked and MD5 sums checked
checking for gcc... gcc46 -std=gnu99
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 gcc46 -std=gnu99 accepts -g... yes
checking for gcc46 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc46 -std=gnu99 -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... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc46 -std=gnu99 supports static inline...
yes
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/local/bin/java'
archiver    : '/usr/local/bin/jar'
compiler    : '/usr/local/bin/javac'
header prep.: '/usr/local/bin/javah'
cpp flags   : '-I/usr/local/jdk1.6.0/jre/../include
-I/usr/local/jdk1.6.0/jre/../include/freebsd'
java libs   : '-L/usr/local/jdk1.6.0/jre/lib/i386/server
-L/usr/local/jdk1.6.0/jre/lib/i386
-L/usr/local/jdk1.6.0/jre/../lib/i386 -L -L/usr/java/packages/lib/i386
-L/lib -L/usr/lib -L/usr/local/lib -ljvm'
checking whether JNI programs can be compiled... yes
checking JNI data types... ok
checking whether JRI should be compiled (autodetect)... yes
checking whether debugging output should be enabled... no
checking whether memory profiling is desired... no
checking whether threads support is requested... no
checking whether callbacks support is requested... no
checking whether JNI cache support is requested... no
checking whether JRI is requested... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status: creating src/config.h
=== configuring in jri (/tmp/RtmpiB6MRQ/R.INSTALL7b063a/rJava/jri)
configure: running /bin/sh ./configure '--prefix=/usr/local'
--cache-file=/dev/null --srcdir=.
checking build system type... i386-unknown-freebsd9.0
checking host system type... i386-unknown-freebsd9.0
checking for gcc... gcc46 -std=gnu99
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 gcc46 -std=gnu99 accepts -g... yes
checking for gcc46 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... cpp
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... yes
checking whether Java interpreter works... checking whether JNI
programs can be compiled... yes
checking whether JNI programs can be run... yes
checking JNI data types... ok
checking whether Rinterface.h exports R_CStackXXX variables... yes
checking whether Rinterface.h exports R_SignalHandlers... yes
configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating Makefile
config.status: creating run
config.status: creating src/config.h
** libs
gcc46 -std=gnu99 -I/usr/local/lib/R/include -I.
-I/usr/local/jdk1.6.0/jre/../include
-I/usr/local/jdk1.6.0/jre/../include/freebsd     -fpic  -O2 -pipe
-Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c Rglue.c -o
Rglue.o
gcc46 -std=gnu99 -I/usr/local/lib/R/include -I.
-I/usr/local/jdk1.6.0/jre/../include
-I/usr/local/jdk1.6.0/jre/../include/freebsd     -fpic  -O2 -pipe
-Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c arrayc.c -o
arrayc.o
gcc46 -std=gnu99 -I/usr/local/lib/R/include -I.
-I/usr/local/jdk1.6.0/jre/../include
-I/usr/local/jdk1.6.0/jre/../include/freebsd     -fpic  -O2 -pipe
-Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c callJNI.c -o
callJNI.o
gcc46 -std=gnu99 -I/usr/local/lib/R/include -I.
-I/usr/local/jdk1.6.0/jre/../include
-I/usr/local/jdk1.6.0/jre/../include/freebsd     -fpic  -O2 -pipe
-Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c callback.c -o
callback.o
gcc46 -std=gnu99 -I/usr/local/lib/R/include -I.
-I/usr/local/jdk1.6.0/jre/../include
-I/usr/local/jdk1.6.0/jre/../include/freebsd     -fpic  -O2 -pipe
-Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c fields.c -o
fields.o
gcc46 -std=gnu99 -I/usr/local/lib/R/include -I.
-I/usr/local/jdk1.6.0/jre/../include
-I/usr/local/jdk1.6.0/jre/../include/freebsd     -fpic  -O2 -pipe
-Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c init.c -o
init.o
gcc46 -std=gnu99 -I/usr/local/lib/R/include -I.
-I/usr/local/jdk1.6.0/jre/../include
-I/usr/local/jdk1.6.0/jre/../include/freebsd     -fpic  -O2 -pipe
-Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c jri_glue.c -o
jri_glue.o
jri_glue.c: In function 'PushToREXP':
jri_glue.c:24:15: warning: cast from pointer to integer of different
size [-Wpointer-to-int-cast]
jri_glue.c: In function 'RReleaseREXP':
jri_glue.c:52:11: warning: cast to pointer from integer of different
size [-Wint-to-pointer-cast]
gcc46 -std=gnu99 -I/usr/local/lib/R/include -I.
-I/usr/local/jdk1.6.0/jre/../include
-I/usr/local/jdk1.6.0/jre/../include/freebsd     -fpic  -O2 -pipe
-Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c loader.c -o
loader.o
gcc46 -std=gnu99 -I/usr/local/lib/R/include -I.
-I/usr/local/jdk1.6.0/jre/../include
-I/usr/local/jdk1.6.0/jre/../include/freebsd     -fpic  -O2 -pipe
-Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c otables.c -o
otables.o
gcc46 -std=gnu99 -I/usr/local/lib/R/include -I.
-I/usr/local/jdk1.6.0/jre/../include
-I/usr/local/jdk1.6.0/jre/../include/freebsd     -fpic  -O2 -pipe
-Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c rJava.c -o
rJava.o
gcc46 -std=gnu99 -I/usr/local/lib/R/include -I.
-I/usr/local/jdk1.6.0/jre/../include
-I/usr/local/jdk1.6.0/jre/../include/freebsd     -fpic  -O2 -pipe
-Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c tools.c -o
tools.o
gcc46 -std=gnu99 -fpic -shared -Wl,-rpath=/usr/local/lib/gcc46 -o
rJava.so Rglue.o arrayc.o callJNI.o callback.o fields.o init.o
jri_glue.o loader.o otables.o rJava.o tools.o
-L/usr/local/jdk1.6.0/jre/lib/i386/server
-L/usr/local/jdk1.6.0/jre/lib/i386
-L/usr/local/jdk1.6.0/jre/../lib/i386 -L -L/usr/java/packages/lib/i386
-L/lib -L/usr/lib -L/usr/local/lib -ljvm -L/usr/local/lib/R/lib -lR
(cd ../jri && make)
make -C src JRI.jar
/usr/local/bin/javac -target 1.4 -source 1.4 -d .
realpath: : No such file or directory
javac: no source files
Usage: javac <options> <source files>
use -help for a list of possible options
*** Error code 2

Stop in /tmp/RtmpiB6MRQ/R.INSTALL7b063a/rJava/jri/src.
*** Error code 1

Stop in /tmp/RtmpiB6MRQ/R.INSTALL7b063a/rJava/jri.
*** Error code 1

Stop in /tmp/RtmpiB6MRQ/R.INSTALL7b063a/rJava/src.
ERROR: compilation failed for package 'rJava'
* removing '/usr/local/lib/R/library/rJava'

The downloaded packages are in
        '/tmp/Rtmp5Eg6iF/downloaded_packages'
Updating HTML index of packages in '.Library'
Making packages.html  ... done
Warning message:
In install.packages("rJava") :
  installation of package 'rJava' had non-zero exit status
>

... and I'm now at a loss... Any ideas? Many thanks!

-- 
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