Sorry for this delay. I have installed rjava on Fedora, CentOS and Debians.
The secret is to install java and configure de java variables. The easiest
way for R is:
R CMD javareconf
It will detect your java envoriment and preconfigure R for you.
Then run: R CMD INSTALL rJava etc as you did.
Caveman
On Tue, Feb 8, 2011 at 9:05 AM, Prof Brian Ripley <rip...@stats.ox.ac.uk>wrote:
> This isn't the right place (rJava has its own support lists), but
>
> - that is not the Java package installed on any version of Fedora I have
> seen, and you might want to try the native openjdk version.
>
> - the JAVA_HOME used by the build is not what you show, as it is looking in
> /opt/jre1.6.0_22/include (and needs to look in the JDK).
>
> I have no idea what about your setup caused the discrepancy: please seek
> help from your local Linux support (or use rJava's support lists).
>
>
> On Mon, 7 Feb 2011, servet cizmeli wrote:
>
> I am on a fedora server on which I am not root privileges. I am trying to
>> locally install rJava... Here are my steps :
>>
>> $uname -a
>> Linux 2.6.18-194.17.4.el5 #1 SMP Mon Oct 25 15:50:53 EDT 2010 x86_64
>> x86_64 x86_64 GNU/Linux
>>
>> $ java -version
>> java version "1.6.0_22"
>> Java(TM) SE Runtime Environment (build 1.6.0_22-b04)
>> Java HotSpot(TM) 64-Bit Server VM (build 17.1-b03, mixed mode)
>>
>> $ echo $JAVA_HOME
>> /opt/jdk1.6.0_22/
>>
>> $ R CMD javareconf -e
>> Java interpreter : /opt/jdk1.6.0_22//jre/bin/java
>> Java version : 1.6.0_22
>> Java home path : /opt/jdk1.6.0_22/
>> Java compiler : /opt/jdk1.6.0_22//bin/javac
>> Java headers gen.: /opt/jdk1.6.0_22//bin/javah
>> Java archive tool: /opt/jdk1.6.0_22//bin/jar
>> Java library path:
>> $(JAVA_HOME)jre/lib/amd64/server:$(JAVA_HOME)jre/lib/amd64:$(JAVA_HOME)jre/../lib/amd64::/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
>> JNI linker flags : -L$(JAVA_HOME)jre/lib/amd64/server
>> -L$(JAVA_HOME)jre/lib/amd64 -L$(JAVA_HOME)jre/../lib/amd64 -L
>> -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm
>> JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
>>
>> The following Java variables have been exported:
>> JAVA_HOME JAVA JAVAC JAVAH JAR JAVA_LIBS JAVA_CPPFLAGS
>> JAVA_LD_LIBRARY_PATH
>>
>> And the installation halts with the following error (please see below for
>> the details):
>> rJava.h:19:17: error: jni.h: No such file or directory
>>
>> I would appreciate very much your kindly help
>> Servet
>>
>>
>>
>> install.packages("rJava",dep=T)
>> Installing package(s) into
>> /home/acizmeli/R/x86_64-redhat-linux-gnu-library/2.12
>> (as lib is unspecified)
>> --- Please select a CRAN mirror for use in this session ---
>> Loading Tcl/Tk interface ... done
>> trying URL 'http://cran.skazkaforyou.com/src/contrib/rJava_0.8-8.tar.gz'
>> Content type 'application/x-gzip' length 522057 bytes (509 Kb)
>> opened URL
>> ==================================================
>> downloaded 509 Kb
>>
>> * installing *source* package rJava ...
>> checking for gcc... gcc -m64 -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 -m64 -std=gnu99 accepts -g... yes
>> checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
>> checking how to run the C preprocessor... gcc -m64 -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 -m64 -std=gnu99 supports static inline...
>> yes
>> checking whether setjmp.h is POSIX.1 compatible... yes
>> checking whether sigsetjmp is declared... yes
>> checking whether siglongjmp is declared... yes
>> checking Java support in R... present:
>> interpreter : '/opt/jdk1.6.0_22//jre/bin/java'
>> archiver : '/opt/jdk1.6.0_22//bin/jar'
>> compiler : '/opt/jdk1.6.0_22//bin/javac'
>> header prep.: '/opt/jdk1.6.0_22//bin/javah'
>> cpp flags : '-I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux'
>> java libs : '-L$(JAVA_HOME)jre/lib/amd64/server
>> -L$(JAVA_HOME)jre/lib/amd64 -L$(JAVA_HOME)jre/../lib/amd64 -L
>> -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -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/RtmpUH5YdX/R.INSTALL3e0ff145/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 -m64 -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 -m64 -std=gnu99 accepts -g... yes
>> checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
>> checking how to run the C preprocessor... gcc -m64 -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 -m64 -std=gnu99 -I/usr/include/R -I. -I/opt/jre1.6.0_22/include
>> -I/opt/jre1.6.0_22/include/linux -I/usr/local/include -fpic -O2 -g -pipe
>> -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>> --param=ssp-buffer-size=4 -m64 -mtune=generic -c Rglue.c -o Rglue.o
>> In file included from Rglue.c:2:
>> rJava.h:19:17: error: jni.h: No such file or directory
>> In file included from Rglue.c:2:
>> rJava.h:120: error: expected =, ,, ;, asm or __attribute__
>> before * token
>> rJava.h:122: error: expected =, ,, ;, asm or __attribute__
>> before * token
>> rJava.h:123: error: expected ) before * token
>> rJava.h:124: error: expected ) before * token
>> rJava.h:126: warning: parameter names (without types) in function
>> declaration
>> rJava.h:127: error: expected =, ,, ;, asm or __attribute__
>> before getSimpleClassNames
>> rJava.h:128: warning: parameter names (without types) in function
>> declaration
>> rJava.h:132: error: expected =, ,, ;, asm or __attribute__
>> before * token
>> rJava.h:135: error: expected =, ,, ;, asm or __attribute__
>> before javaStringClass
>> rJava.h:136: error: expected =, ,, ;, asm or __attribute__
>> before javaObjectClass
>> rJava.h:137: error: expected =, ,, ;, asm or __attribute__
>> before javaClassClass
>> rJava.h:138: error: expected =, ,, ;, asm or __attribute__
>> before javaFieldClass
>> rJava.h:139: error: expected =, ,, ;, asm or __attribute__
>> before rj_RJavaTools_Class
>> rJava.h:141: error: expected =, ,, ;, asm or __attribute__
>> before mid_forName
>> rJava.h:142: error: expected =, ,, ;, asm or __attribute__
>> before mid_getName
>> rJava.h:143: error: expected =, ,, ;, asm or __attribute__
>> before mid_getSimpleName
>> rJava.h:144: error: expected =, ,, ;, asm or __attribute__
>> before mid_getSuperclass
>> rJava.h:145: error: expected =, ,, ;, asm or __attribute__
>> before mid_getType
>> rJava.h:146: error: expected =, ,, ;, asm or __attribute__
>> before mid_getField
>> rJava.h:147: error: expected =, ,, ;, asm or __attribute__
>> before mid_rj_getSimpleClassNames
>> rJava.h:149: error: expected =, ,, ;, asm or __attribute__
>> before mid_RJavaTools_getFieldTypeName
>> rJava.h:152: error: expected =, ,, ;, asm or __attribute__
>> before rj_RJavaImport_Class
>> rJava.h:153: error: expected =, ,, ;, asm or __attribute__
>> before mid_RJavaImport_getKnownClasses
>> rJava.h:154: error: expected =, ,, ;, asm or __attribute__
>> before mid_RJavaImport_lookup
>> rJava.h:155: error: expected =, ,, ;, asm or __attribute__
>> before mid_RJavaImport_exists
>> rJava.h:172: error: expected =, ,, ;, asm or __attribute__
>> before getImporterReference
>> rJava.h:178: error: expected =, ,, ;, asm or __attribute__
>> before clClassLoader
>> rJava.h:179: error: expected =, ,, ;, asm or __attribute__
>> before oClassLoader
>> rJava.h:182: error: expected ) before * token
>> rJava.h:183: error: expected ) before * token
>> rJava.h:184: error: expected =, ,, ;, asm or __attribute__
>> before R1par2jvalue
>> rJava.h:187: error: expected ) before * token
>> rJava.h:188: error: expected ) before * token
>> rJava.h:191: error: expected =, ,, ;, asm or __attribute__
>> before callToString
>> rJava.h:194: error: expected =, ,, ;, asm or __attribute__
>> before createObject
>> rJava.h:195: error: expected =, ,, ;, asm or __attribute__
>> before findClass
>> rJava.h:196: error: expected =, ,, ;, asm or __attribute__
>> before objectClass
>> rJava.h:198: error: expected =, ,, ;, asm or __attribute__
>> before newDoubleArray
>> rJava.h:199: error: expected =, ,, ;, asm or __attribute__
>> before newIntArray
>> rJava.h:200: error: expected =, ,, ;, asm or __attribute__
>> before newBooleanArrayI
>> rJava.h:201: error: expected =, ,, ;, asm or __attribute__
>> before newString
>> rJava.h:202: error: expected =, ,, ;, asm or __attribute__
>> before newCharArrayI
>> rJava.h:203: error: expected =, ,, ;, asm or __attribute__
>> before newShortArrayI
>> rJava.h:204: error: expected =, ,, ;, asm or __attribute__
>> before newFloatArrayD
>> rJava.h:205: error: expected =, ,, ;, asm or __attribute__
>> before newLongArrayD
>> rJava.h:206: error: expected =, ,, ;, asm or __attribute__
>> before newByteArray
>> rJava.h:207: error: expected =, ,, ;, asm or __attribute__
>> before newByteArrayI
>> rJava.h:209: error: expected =, ,, ;, asm or __attribute__
>> before makeGlobal
>> rJava.h:210: error: expected ) before * token
>> rJava.h:211: error: expected ) before * token
>> rJava.h:213: error: expected ) before * token
>> rJava.h:215: error: expected ) before * token
>> rJava.h:217: 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:777: error: expected ) before * token
>> Rglue.c:789: error: expected ) before * token
>> Rglue.c:808: error: expected ) before * token
>> Rglue.c:831: error: expected ) before * token
>> Rglue.c: In function RcreateArray:
>> Rglue.c:857: error: JNIEnv undeclared (first use in this function)
>> Rglue.c:857: error: env undeclared (first use in this function)
>> Rglue.c:864: error: jbyteArray undeclared (first use in this function)
>> Rglue.c:864: error: expected ; before a
>> Rglue.c:865: error: a undeclared (first use in this function)
>> Rglue.c:866: warning: implicit declaration of function new_jarrayRef
>> Rglue.c:866: warning: return makes pointer from integer without a cast
>> Rglue.c:868: error: jcharArray undeclared (first use in this function)
>> Rglue.c:868: error: expected ; before a
>> Rglue.c:870: warning: return makes pointer from integer without a cast
>> Rglue.c:872: error: jintArray undeclared (first use in this function)
>> Rglue.c:872: error: expected ; before a
>> Rglue.c:874: warning: return makes pointer from integer without a cast
>> Rglue.c:880: error: jfloatArray undeclared (first use in this function)
>> Rglue.c:880: error: expected ; before a
>> Rglue.c:882: warning: return makes pointer from integer without a cast
>> Rglue.c:884: error: jlongArray undeclared (first use in this function)
>> Rglue.c:884: error: expected ; before a
>> Rglue.c:886: warning: return makes pointer from integer without a cast
>> Rglue.c:888: error: jdoubleArray undeclared (first use in this function)
>> Rglue.c:888: error: expected ; before a
>> Rglue.c:890: warning: return makes pointer from integer without a cast
>> Rglue.c:895: error: jobjectArray undeclared (first use in this function)
>> Rglue.c:895: error: expected ; before a
>> Rglue.c:899: error: jobject undeclared (first use in this function)
>> Rglue.c:899: error: expected ; before so
>> Rglue.c:900: error: so undeclared (first use in this function)
>> Rglue.c:904: warning: return makes pointer from integer without a cast
>> Rglue.c:909: error: jbooleanArray undeclared (first use in this
>> function)
>> Rglue.c:909: error: expected ; before a
>> Rglue.c:911: warning: return makes pointer from integer without a cast
>> Rglue.c:916: error: jclass undeclared (first use in this function)
>> Rglue.c:916: error: expected ; before ac
>> Rglue.c:933: error: ac undeclared (first use in this function)
>> Rglue.c:953: error: expected ; before a
>> Rglue.c:955: error: javaObjectClass undeclared (first use in this
>> function)
>> Rglue.c:960: error: expected ; before o
>> Rglue.c:965: error: o undeclared (first use in this function)
>> Rglue.c:971: warning: return makes pointer from integer without a cast
>> Rglue.c:976: error: expected ; before a
>> Rglue.c:978: warning: return makes pointer from integer without a cast
>> Rglue.c: In function RpollException:
>> Rglue.c:988: error: JNIEnv undeclared (first use in this function)
>> Rglue.c:988: error: env undeclared (first use in this function)
>> Rglue.c:989: error: jthrowable undeclared (first use in this function)
>> Rglue.c:989: error: expected ; before t
>> Rglue.c:991: error: t undeclared (first use in this function)
>> Rglue.c: In function RclearException:
>> Rglue.c:999: error: JNIEnv undeclared (first use in this function)
>> Rglue.c:999: error: env undeclared (first use in this function)
>> Rglue.c: In function RthrowException:
>> Rglue.c:1020: error: JNIEnv undeclared (first use in this function)
>> Rglue.c:1020: error: env undeclared (first use in this function)
>> Rglue.c:1021: error: jthrowable undeclared (first use in this function)
>> Rglue.c:1021: error: expected ; before t
>> Rglue.c:1032: error: t undeclared (first use in this function)
>> make: *** [Rglue.o] Error 1
>> ERROR: compilation failed for package rJava
>> * removing /home/acizmeli/R/x86_64-redhat-linux-gnu-library/2.12/rJava
>>
>> The downloaded packages are in
>> /tmp/Rtmpr5x7PM/downloaded_packages
>> Warning message:
>> In install.packages("rJava", dep = T) :
>> installation of package 'rJava' had non-zero exit status
>>
>> ______________________________________________
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
> --
> Brian D. Ripley, rip...@stats.ox.ac.uk
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UK Fax: +44 1865 272595
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
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______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
