From mwkimpel at gmail.com  Wed Jul 15 20:46:55 2009
From: mwkimpel at gmail.com (Mark Kimpel)
Date: Wed, 15 Jul 2009 14:46:55 -0400
Subject: [Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian
	Lenny
Message-ID: <6b93d1830907151146q506e937fxd4d31cc7d01c2ea3@mail.gmail.com>

I have been futzing around for days tying to get rJava to install on
my freshly build Debian Lenny installation. I have R-2.9.1 installed
from source in my R_HOME directory and R-2.7.1 installed via apt-get
install r-recommended. I was tried many different things, but by
accident started up R-2.7.1 as root and viola, successful install. I
immediately exited out of R-2.7.1 and started R-2.9.1 as root and
compilation fails. The file

The output is voluminous, but is included below. I had originally
thought that my problem had to do with setting environmental
variables, but now it seems not.

Thanks,
Mark

mkimpel-debian-xps /usr/lib/jvm/java-6-sun/include: su root
Password:
mkimpel-debian-xps:/usr/lib/jvm/java-6-sun/include#
/home/mkimpel/R_HOME/R-2.9.1/R-build/bin/R
WARNING: ignoring environment value of R_HOME

R version 2.9.1 (2009-06-26)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages('rJava')
Warning in install.packages("rJava") :
  argument 'lib' is missing: using '/usr/local/lib/R/site-library'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.fhcrc.org/src/contrib/rJava_0.6-3.tar.gz'
Content type 'application/x-gzip' length 240527 bytes (234 Kb)
opened URL
==================================================
downloaded 234 Kb

* Installing *source* package ?rJava? ...
checking for gcc... gcc -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 gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /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 gcc -std=gnu99 supports static inline...
yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver    : '/usr/bin/jar'
compiler    : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags   : '-I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux'
java libs   : '-L$(JAVA_HOME)/lib/amd64/server
-L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm'
checking whether JNI programs can be compiled... yes
checking JNI data types... ok
checking whether JRI should be compiled (autodetect)... no
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... no
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status: creating src/config.h
** libs
gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.1/R-build/lib64/R/include
-I. -I/usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../include
-I/usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../include/linux
-I/usr/local/include    -fpic  -g -O2 -c Rglue.c -o Rglue.o
In file included from Rglue.c:2:
rJava.h:17:17: error: jni.h: No such file or directory
In file included from Rglue.c:2:
rJava.h:115: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?*? token
rJava.h:117: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?*? token
rJava.h:120: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?*? token
rJava.h:122: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?javaStringClass?
rJava.h:123: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?javaObjectClass?
rJava.h:124: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?javaClassClass?
rJava.h:125: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?javaFieldClass?
rJava.h:127: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?mid_forName?
rJava.h:128: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?mid_getName?
rJava.h:129: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?mid_getType?
rJava.h:130: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?mid_getField?
rJava.h:133: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?clClassLoader?
rJava.h:134: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?oClassLoader?
rJava.h:137: error: expected ?)? before ?*? token
rJava.h:138: error: expected ?)? before ?*? token
rJava.h:139: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?R1par2jvalue?
rJava.h:144: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?callToString?
rJava.h:147: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?createObject?
rJava.h:148: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?findClass?
rJava.h:149: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?objectClass?
rJava.h:151: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?newDoubleArray?
rJava.h:152: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?newIntArray?
rJava.h:153: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?newBooleanArrayI?
rJava.h:154: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?newString?
rJava.h:155: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?newCharArrayI?
rJava.h:156: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?newShortArrayI?
rJava.h:157: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?newFloatArrayD?
rJava.h:158: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?newLongArrayD?
rJava.h:159: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?newByteArray?
rJava.h:160: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?newByteArrayI?
rJava.h:162: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?makeGlobal?
rJava.h:163: error: expected ?)? before ?*? token
rJava.h:164: error: expected ?)? before ?*? token
rJava.h:166: error: expected ?)? before ?*? token
rJava.h:168: error: expected ?)? before ?*? token
rJava.h:170: error: expected ?)? before ?*? token
Rglue.c: In function ?JRefObjectFinalizer?:
Rglue.c:79: error: ?JNIEnv? undeclared (first use in this function)
Rglue.c:79: error: (Each undeclared identifier is reported only once
Rglue.c:79: error: for each function it appears in.)
Rglue.c:79: error: ?env? undeclared (first use in this function)
Rglue.c:79: warning: implicit declaration of function ?getJNIEnv?
Rglue.c:80: error: ?jobject? undeclared (first use in this function)
Rglue.c:80: error: expected ?;? before ?o?
Rglue.c:95: error: ?o? undeclared (first use in this function)
Rglue.c:98: warning: implicit declaration of function ?releaseGlobal?
Rglue.c: At top level:
Rglue.c:104: error: expected ?)? before ?*? token
Rglue.c: In function ?deserializeSEXP?:
Rglue.c:151: error: ?JNIEnv? undeclared (first use in this function)
Rglue.c:151: error: ?env? undeclared (first use in this function)
Rglue.c:152: error: ?clClassLoader? undeclared (first use in this function)
Rglue.c:152: error: ?oClassLoader? undeclared (first use in this function)
Rglue.c:153: error: ?jbyteArray? undeclared (first use in this function)
Rglue.c:153: error: expected ?;? before ?ser?
Rglue.c:154: error: ?ser? undeclared (first use in this function)
Rglue.c:155: error: ?jmethodID? undeclared (first use in this function)
Rglue.c:155: error: expected ?;? before ?mid?
Rglue.c:156: error: ?mid? undeclared (first use in this function)
Rglue.c:157: error: ?jobject? undeclared (first use in this function)
Rglue.c:157: error: expected ?;? before ?res?
Rglue.c:158: error: ?res? undeclared (first use in this function)
Rglue.c:159: error: expected ?;? before ?go?
Rglue.c:161: error: ?go? undeclared (first use in this function)
Rglue.c:173: warning: implicit declaration of function ?releaseObject?
Rglue.c: At top level:
Rglue.c:214: error: expected ?)? before ?*? token
Rglue.c:380: error: expected ?)? before ?*? token
Rglue.c:390: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__?
before ?R1par2jvalue?
Rglue.c: In function ?RcallMethod?:
Rglue.c:410: error: ?jvalue? undeclared (first use in this function)
Rglue.c:410: error: expected ?;? before ?jpar?
Rglue.c:411: error: ?jobject? undeclared (first use in this function)
Rglue.c:411: error: expected ?;? before ?tmpo?
Rglue.c:412: error: expected ?;? before ?o?
Rglue.c:414: error: ?jmethodID? undeclared (first use in this function)
Rglue.c:414: error: expected ?;? before ?mid?
Rglue.c:415: error: ?jclass? undeclared (first use in this function)
Rglue.c:415: error: expected ?;? before ?cls?
Rglue.c:416: error: ?JNIEnv? undeclared (first use in this function)
Rglue.c:416: error: ?env? undeclared (first use in this function)
Rglue.c:424: error: ?o? undeclared (first use in this function)
Rglue.c:440: error: ?cls? undeclared (first use in this function)
Rglue.c:440: warning: implicit declaration of function ?findClass?
Rglue.c:442: warning: implicit declaration of function ?objectClass?
Rglue.c:467: warning: implicit declaration of function ?Rpar2jvalue?
Rglue.c:467: error: ?jpar? undeclared (first use in this function)
Rglue.c:467: error: ?tmpo? undeclared (first use in this function)
Rglue.c:471: error: ?mid? undeclared (first use in this function)
Rglue.c:475: warning: implicit declaration of function ?checkExceptionsX?
Rglue.c:481: warning: implicit declaration of function ?Rfreejpars?
Rglue.c:542: error: ?jlong? undeclared (first use in this function)
Rglue.c:542: error: expected ?;? before ?r?
Rglue.c:546: error: ?r? undeclared (first use in this function)
Rglue.c:555: error: ?jshort? undeclared (first use in this function)
Rglue.c:555: error: expected ?;? before ?r?
Rglue.c:568: error: ?jboolean? undeclared (first use in this function)
Rglue.c:568: error: expected ?;? before ?r?
Rglue.c:607: error: expected ?;? before ?r?
Rglue.c:620: warning: implicit declaration of function ?j2SEXP?
Rglue.c:620: warning: assignment makes pointer from integer without a cast
Rglue.c: In function ?RcallSyncMethod?:
Rglue.c:634: error: ?jobject? undeclared (first use in this function)
Rglue.c:634: error: expected ?;? before ?o?
Rglue.c:635: error: ?JNIEnv? undeclared (first use in this function)
Rglue.c:635: error: ?env? undeclared (first use in this function)
Rglue.c:642: error: ?o? undeclared (first use in this function)
Rglue.c:650: error: ?JNI_OK? undeclared (first use in this function)
Rglue.c: In function ?RcreateObject?:
Rglue.c:671: error: ?jvalue? undeclared (first use in this function)
Rglue.c:671: error: expected ?;? before ?jpar?
Rglue.c:672: error: ?jobject? undeclared (first use in this function)
Rglue.c:672: error: expected ?;? before ?tmpo?
Rglue.c:673: error: expected ?;? before ?o?
Rglue.c:674: error: ?JNIEnv? undeclared (first use in this function)
Rglue.c:674: error: ?env? undeclared (first use in this function)
Rglue.c:690: error: ?jpar? undeclared (first use in this function)
Rglue.c:690: error: ?tmpo? undeclared (first use in this function)
Rglue.c:704: error: ?o? undeclared (first use in this function)
Rglue.c:704: warning: implicit declaration of function ?createObject?
Rglue.c:723: warning: return makes pointer from integer without a cast
Rglue.c: At top level:
Rglue.c:727: error: expected ?)? before ?*? token
Rglue.c:758: error: expected ?)? before ?*? token
Rglue.c:770: error: expected ?)? before ?*? token
Rglue.c: In function ?RcreateArray?:
Rglue.c:786: error: ?JNIEnv? undeclared (first use in this function)
Rglue.c:786: error: ?env? undeclared (first use in this function)
Rglue.c:793: error: ?jbyteArray? undeclared (first use in this function)
Rglue.c:793: error: expected ?;? before ?a?
Rglue.c:794: error: ?a? undeclared (first use in this function)
Rglue.c:795: warning: implicit declaration of function ?new_jarrayRef?
Rglue.c:795: warning: return makes pointer from integer without a cast
Rglue.c:797: error: ?jcharArray? undeclared (first use in this function)
Rglue.c:797: error: expected ?;? before ?a?
Rglue.c:799: warning: return makes pointer from integer without a cast
Rglue.c:801: error: ?jintArray? undeclared (first use in this function)
Rglue.c:801: error: expected ?;? before ?a?
Rglue.c:803: warning: return makes pointer from integer without a cast
Rglue.c:809: error: ?jfloatArray? undeclared (first use in this function)
Rglue.c:809: error: expected ?;? before ?a?
Rglue.c:811: warning: return makes pointer from integer without a cast
Rglue.c:813: error: ?jlongArray? undeclared (first use in this function)
Rglue.c:813: error: expected ?;? before ?a?
Rglue.c:815: warning: return makes pointer from integer without a cast
Rglue.c:817: error: ?jdoubleArray? undeclared (first use in this function)
Rglue.c:817: error: expected ?;? before ?a?
Rglue.c:819: warning: return makes pointer from integer without a cast
Rglue.c:824: error: ?jobjectArray? undeclared (first use in this function)
Rglue.c:824: error: expected ?;? before ?a?
Rglue.c:828: error: ?jobject? undeclared (first use in this function)
Rglue.c:828: error: expected ?;? before ?so?
Rglue.c:829: error: ?so? undeclared (first use in this function)
Rglue.c:833: warning: return makes pointer from integer without a cast
Rglue.c:838: error: ?jbooleanArray? undeclared (first use in this function)
Rglue.c:838: error: expected ?;? before ?a?
Rglue.c:840: warning: return makes pointer from integer without a cast
Rglue.c:845: error: ?jclass? undeclared (first use in this function)
Rglue.c:845: error: expected ?;? before ?ac?
Rglue.c:861: error: ?ac? undeclared (first use in this function)
Rglue.c:881: error: expected ?;? before ?a?
Rglue.c:883: error: ?javaObjectClass? undeclared (first use in this function)
Rglue.c:888: error: expected ?;? before ?o?
Rglue.c:893: error: ?o? undeclared (first use in this function)
Rglue.c:899: warning: return makes pointer from integer without a cast
Rglue.c:904: error: expected ?;? before ?a?
Rglue.c:906: warning: return makes pointer from integer without a cast
Rglue.c: In function ?RpollException?:
Rglue.c:916: error: ?JNIEnv? undeclared (first use in this function)
Rglue.c:916: error: ?env? undeclared (first use in this function)
Rglue.c:917: error: ?jthrowable? undeclared (first use in this function)
Rglue.c:917: error: expected ?;? before ?t?
Rglue.c:919: error: ?t? undeclared (first use in this function)
Rglue.c: In function ?RclearException?:
Rglue.c:927: error: ?JNIEnv? undeclared (first use in this function)
Rglue.c:927: error: ?env? undeclared (first use in this function)
Rglue.c: In function ?RthrowException?:
Rglue.c:948: error: ?JNIEnv? undeclared (first use in this function)
Rglue.c:948: error: ?env? undeclared (first use in this function)
Rglue.c:949: error: ?jthrowable? undeclared (first use in this function)
Rglue.c:949: error: expected ?;? before ?t?
Rglue.c:960: error: ?t? undeclared (first use in this function)
make: *** [Rglue.o] Error 1
ERROR: compilation failed for package ?rJava?
* Removing ?/usr/local/lib/R/site-library/rJava?
* Restoring previous ?/usr/local/lib/R/site-library/rJava?

The downloaded packages are in
	?/tmp/Rtmp0D1hWd/downloaded_packages?
Warning message:
In install.packages("rJava") :
  installation of package 'rJava' had non-zero exit status
> q()
Save workspace image? [y/n/c]: n
mkimpel-debian-xps:/usr/lib/jvm/java-6-sun/include# R

R version 2.7.1 (2008-06-23)
Copyright (C) 2008 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages('rJava')
Warning in install.packages("rJava") :
  argument 'lib' is missing: using '/usr/local/lib/R/site-library'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.fhcrc.org/src/contrib/rJava_0.6-3.tar.gz'
Content type 'application/x-gzip' length 240527 bytes (234 Kb)
opened URL
==================================================
downloaded 234 Kb

* Installing *source* package 'rJava' ...
checking for gcc... gcc -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 gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /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 gcc -std=gnu99 supports static inline...
yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver    : '/usr/bin/jar'
compiler    : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags   : '-I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux'
java libs   : '-L$(JAVA_HOME)/lib/amd64/server
-L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/lib -L/usr/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/R.INSTALL.bELNGf/rJava/jri)
configure: running /bin/sh ./configure '--prefix=/usr/local'
--cache-file=/dev/null --srcdir=.
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc -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 gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /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
gcc -std=gnu99 -I/usr/share/R/include -I.
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux     -fpic  -g
-O2 -c arrayc.c -o arrayc.o
gcc -std=gnu99 -I/usr/share/R/include -I.
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux     -fpic  -g
-O2 -c callback.c -o callback.o
gcc -std=gnu99 -I/usr/share/R/include -I.
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux     -fpic  -g
-O2 -c callJNI.c -o callJNI.o
gcc -std=gnu99 -I/usr/share/R/include -I.
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux     -fpic  -g
-O2 -c fields.c -o fields.o
gcc -std=gnu99 -I/usr/share/R/include -I.
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux     -fpic  -g
-O2 -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -I.
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux     -fpic  -g
-O2 -c jri_glue.c -o jri_glue.o
gcc -std=gnu99 -I/usr/share/R/include -I.
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux     -fpic  -g
-O2 -c loader.c -o loader.o
gcc -std=gnu99 -I/usr/share/R/include -I.
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux     -fpic  -g
-O2 -c Rglue.c -o Rglue.o
gcc -std=gnu99 -I/usr/share/R/include -I.
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux     -fpic  -g
-O2 -c rJava.c -o rJava.o
gcc -std=gnu99 -I/usr/share/R/include -I.
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux     -fpic  -g
-O2 -c tools.c -o tools.o
gcc -std=gnu99 -shared  -o rJava.so arrayc.o callback.o callJNI.o
fields.o init.o jri_glue.o loader.o Rglue.o rJava.o tools.o
-L/usr/lib/jvm/java-6-sun-1.6.0.12/jre/lib/amd64/server
-L/usr/lib/jvm/java-6-sun-1.6.0.12/jre/lib/amd64
-L/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm
-L/usr/lib64/R/lib -lR
make -C ../jri/
make[1]: Entering directory `/tmp/R.INSTALL.bELNGf/rJava/jri'
make -C src JRI.jar
make[2]: Entering directory `/tmp/R.INSTALL.bELNGf/rJava/jri/src'
/usr/bin/javac -target 1.4 -source 1.4 -d . ../Mutex.java
../RBool.java ../RConsoleOutputStream.java ../Rengine.java
../REXP.java ../RFactor.java ../RList.java ../RMainLoopCallbacks.java
../RVector.java
/usr/bin/javah -d . -classpath . org.rosuda.JRI.Rengine
gcc -std=gnu99 -c -o Rengine.o Rengine.c -g -Iinclude
-DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux  -fpic
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux
-I/usr/share/R/include -I/usr/share/R/include -I/usr/share/R/include
gcc -std=gnu99 -c -o jri.o jri.c -g -Iinclude  -DRIF_HAS_CSTACK
-DRIF_HAS_RSIGHAND -g -O2
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux  -fpic
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux
-I/usr/share/R/include -I/usr/share/R/include -I/usr/share/R/include
jri.c: In function ?jri_getObjectArray?:
jri.c:303: warning: cast from pointer to integer of different size
gcc -std=gnu99 -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude
-DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux  -fpic
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux
-I/usr/share/R/include -I/usr/share/R/include -I/usr/share/R/include
gcc -std=gnu99 -c -o Rinit.o Rinit.c -g -Iinclude  -DRIF_HAS_CSTACK
-DRIF_HAS_RSIGHAND -g -O2
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux  -fpic
-I/usr/share/R/include -I/usr/share/R/include -I/usr/share/R/include
gcc -std=gnu99 -c -o globals.o globals.c -g -Iinclude
-DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux  -fpic
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux
gcc -std=gnu99 -c -o rjava.o rjava.c -g -Iinclude  -DRIF_HAS_CSTACK
-DRIF_HAS_RSIGHAND -g -O2
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux  -fpic
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../include/linux
gcc -std=gnu99 -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o
globals.o rjava.o  -shared
-L/usr/lib/jvm/java-6-sun-1.6.0.12/jre/lib/amd64/server
-L/usr/lib/jvm/java-6-sun-1.6.0.12/jre/lib/amd64
-L/usr/lib/jvm/java-6-sun-1.6.0.12/jre/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm
-L/usr/lib64/R/lib -lR
/usr/bin/javac -target 1.4 -source 1.4 -d . ../Mutex.java
../RBool.java ../RConsoleOutputStream.java ../Rengine.java
../REXP.java ../RFactor.java ../RList.java ../RMainLoopCallbacks.java
../RVector.java
/usr/bin/jar fc JRI.jar org libjri.so
make[2]: Leaving directory `/tmp/R.INSTALL.bELNGf/rJava/jri/src'
rm -f libjri.so
cp src/libjri.so libjri.so
/usr/bin/javac -target 1.4 -source 1.4 -classpath src/JRI.jar -d
examples examples/rtest2.java
Note: examples/rtest2.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
/usr/bin/javac -target 1.4 -source 1.4 -classpath src/JRI.jar -d
examples examples/rtest.java
Note: examples/rtest.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
make[1]: Leaving directory `/tmp/R.INSTALL.bELNGf/rJava/jri'
** R
** inst
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'rJava'
     Formats: text html latex example
  accessOp                          text    html    latex   example
  jarray                            text    html    latex   example
  jarrayRef-class                   text    html    latex
  jcall                             text    html    latex   example
  jcast                             text    html    latex   example
  jcastToArray                      text    html    latex   example
  jcheck                            text    html    latex   example
  jengine                           text    html    latex   example
  jequals                           text    html    latex   example
  jfield                            text    html    latex   example
  jfloat-class                      text    html    latex
  jfloat                            text    html    latex
  jinit                             text    html    latex   example
  jmemprof                          text    html    latex   example
  jnew                              text    html    latex   example
  jnull                             text    html    latex   example
  jobjRef-class                     text    html    latex
  jpackage                          text    html    latex   example
  jreflection                       text    html    latex   example
  jserialize                        text    html    latex
  jsimplify                         text    html    latex   example
  loader                            text    html    latex   example
  show                              text    html    latex
** building package indices ...
* DONE (rJava)

The downloaded packages are in
	/tmp/RtmplOpZ4F/downloaded_packages
> q()
Save workspace image? [y/n/c]: n
mkimpel-debian-xps:/usr/lib/jvm/java-6-sun/include#
------------------------------------------------------------
Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail

"The real problem is not whether machines think but whether men do."
-- B. F. Skinner



[Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian Lenny
Mark Kimpel