[Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian Lenny
Mark Kimpel
mwkimpel at gmail.com
Wed Jul 15 20:52:16 CEST 2009
Sorry, My sentence that starts "The file" was truncated and should say
"The file "jni.h" is present and on my PATH, see output below"
mkimpel-debian-xps /usr/lib/jvm/java-6-sun/include: ls
classfile_constants.h jawt.h jdwpTransport.h jni.h jvmti.h linux
mkimpel-debian-xps /usr/lib/jvm/java-6-sun/include: printenv PATH
/home/mkimpel/bin:/usr/local/bin:/usr/bin:/bin:/usr/games:/usr/lib/jvm/
mkimpel-debian-xps /usr/lib/jvm/java-6-sun/include:
------------------------------------------------------------
On Wed, Jul 15, 2009 at 2:46 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
> ******************************************************************
>
More information about the R-devel
mailing list