From josh.m.ulrich at gmail.com  Wed Jul 15 21:13:43 2009
From: josh.m.ulrich at gmail.com (Joshua Ulrich)
Date: Wed, 15 Jul 2009 14:13:43 -0500
Subject: [Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on
	Debian Lenny
In-Reply-To: <6b93d1830907151146q506e937fxd4d31cc7d01c2ea3@mail.gmail.com>
References: <6b93d1830907151146q506e937fxd4d31cc7d01c2ea3@mail.gmail.com>
Message-ID: <8cca69990907151213v440b7046r883d5aff5ea2aad1@mail.gmail.com>

Hi Mark,

The first thing that jumps out to me is that 2.7.1 compiles JRI, while
2.9.1 does not (for some reason, autodetect decides not to compile).

HTH,
Josh
--
http://www.fosstrading.com



On Wed, Jul 15, 2009 at 1:46 PM, Mark Kimpel<mwkimpel at gmail.com> wrote:
> 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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian Lenny
Joshua Ulrich