[Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian Lenny
Joshua Ulrich
josh.m.ulrich at gmail.com
Wed Jul 15 21:13:43 CEST 2009
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
>
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