Dear Orvalho Augusto, Thanks for your response. But we met a new problem. We set as waht you said in the last email and run installing agian. But we got the error: rJava.h:22:17: error: jni.h: No such file or directory. Actually we had found "jni.h" under {JAVA_HOME}/../include and the path had been set in "JNI linker flags". So we so confuded.
Thanks, Jiacheng The below is the detail information. commandline $ R CMD INSTALL rJava_0.9-0.tar.gz output: * installing to library /data1/mri_researchers/wexler_data/jiacheng/R-2.12.0/library * 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 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 : '/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/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)... 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/data1/mri_researchers/wexler_data/jiacheng/R-2.12.0/include -I. -I/usr/java/jre1.6.0_24/../include -I/usr/java/jre1.6.0_24/../include/linux -I/usr/local/include -fpic -g -O2 -c Rglue.c -o Rglue.o In file included from Rglue.c:2: rJava.h:22:17: error: jni.h: No such file or directory In file included from Rglue.c:2: rJava.h:123: error: expected =, ,, ;, asm or __attribute__ before * token rJava.h:125: error: expected =, ,, ;, asm or __attribute__ before * token rJava.h:126: error: expected ) before * token rJava.h:127: error: expected ) before * token rJava.h:129: warning: parameter names (without types) in function declaration rJava.h:130: error: expected =, ,, ;, asm or __attribute__ before getSimpleClassNames rJava.h:131: warning: parameter names (without types) in function declaration rJava.h:135: error: expected =, ,, ;, asm or __attribute__ before * token rJava.h:138: error: expected =, ,, ;, asm or __attribute__ before javaStringClass rJava.h:139: error: expected =, ,, ;, asm or __attribute__ before javaObjectClass rJava.h:140: error: expected =, ,, ;, asm or __attribute__ before javaClassClass rJava.h:141: error: expected =, ,, ;, asm or __attribute__ before javaFieldClass rJava.h:142: error: expected =, ,, ;, asm or __attribute__ before rj_RJavaTools_Class rJava.h:144: error: expected =, ,, ;, asm or __attribute__ before mid_forName rJava.h:145: error: expected =, ,, ;, asm or __attribute__ before mid_getName rJava.h:146: error: expected =, ,, ;, asm or __attribute__ before mid_getSimpleName rJava.h:147: error: expected =, ,, ;, asm or __attribute__ before mid_getSuperclass rJava.h:148: error: expected =, ,, ;, asm or __attribute__ before mid_getType rJava.h:149: error: expected =, ,, ;, asm or __attribute__ before mid_getField rJava.h:150: error: expected =, ,, ;, asm or __attribute__ before mid_rj_getSimpleClassNames rJava.h:152: error: expected =, ,, ;, asm or __attribute__ before mid_RJavaTools_getFieldTypeName rJava.h:155: error: expected =, ,, ;, asm or __attribute__ before rj_RJavaImport_Class rJava.h:156: error: expected =, ,, ;, asm or __attribute__ before mid_RJavaImport_getKnownClasses rJava.h:157: error: expected =, ,, ;, asm or __attribute__ before mid_RJavaImport_lookup rJava.h:158: error: expected =, ,, ;, asm or __attribute__ before mid_RJavaImport_exists rJava.h:175: error: expected =, ,, ;, asm or __attribute__ before getImporterReference rJava.h:181: error: expected =, ,, ;, asm or __attribute__ before clClassLoader rJava.h:182: error: expected =, ,, ;, asm or __attribute__ before oClassLoader rJava.h:185: error: expected ) before * token rJava.h:186: error: expected ) before * token rJava.h:187: error: expected =, ,, ;, asm or __attribute__ before R1par2jvalue rJava.h:190: error: expected ) before * token rJava.h:191: error: expected ) before * token rJava.h:194: error: expected =, ,, ;, asm or __attribute__ before callToString rJava.h:197: error: expected =, ,, ;, asm or __attribute__ before createObject rJava.h:198: error: expected =, ,, ;, asm or __attribute__ before findClass rJava.h:199: error: expected =, ,, ;, asm or __attribute__ before objectClass rJava.h:201: error: expected =, ,, ;, asm or __attribute__ before newDoubleArray rJava.h:202: error: expected =, ,, ;, asm or __attribute__ before newIntArray rJava.h:203: error: expected =, ,, ;, asm or __attribute__ before newBooleanArrayI rJava.h:204: error: expected =, ,, ;, asm or __attribute__ before newString rJava.h:205: error: expected =, ,, ;, asm or __attribute__ before newCharArrayI rJava.h:206: error: expected =, ,, ;, asm or __attribute__ before newShortArrayI rJava.h:207: error: expected =, ,, ;, asm or __attribute__ before newFloatArrayD rJava.h:208: error: expected =, ,, ;, asm or __attribute__ before newLongArrayD rJava.h:209: error: expected =, ,, ;, asm or __attribute__ before newByteArray rJava.h:210: error: expected =, ,, ;, asm or __attribute__ before newByteArrayI rJava.h:212: error: expected =, ,, ;, asm or __attribute__ before makeGlobal rJava.h:213: error: expected ) before * token rJava.h:214: error: expected ) before * token rJava.h:216: error: expected ) before * token rJava.h:218: error: expected ) before * token rJava.h:220: 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 /R-2.12.0/library/rJava On Fri, Mar 18, 2011 at 4:59 PM, Orvalho Augusto <orvaq...@gmail.com> wrote: > It seems that you are not alone with that error ( > http://stackoverflow.com/questions/3311940/r-rjava-package-install-failing > ). > > Defining only JAVA_HOME he would find everything else. > > Backup your /etc/R before do this. > > Running the R CMD javareconf is to place variables like this in > /etc/R/Makeconf (hope the experts corect me) > JAR = /usr/bin/jar > JAVA = /usr/bin/java > JAVAC = /usr/bin/javac > JAVAH = /usr/bin/javah > JAVA_HOME = /usr/lib/jvm/java-6-sun-1.6.0.24/jre > JAVA_LD_LIBRARY_PATH = > $(JAVA_HOME)/lib/i386/server:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386:/usr/java/packages/lib/i386:/lib:/usr/lib > JAVA_LIBS = -L$(JAVA_HOME)/lib/i386/server -L$(JAVA_HOME)/lib/i386 > -L$(JAVA_HOME)/../lib/i386 -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib > -ljvm > JAVA_CPPFLAGS = -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux > > Add it manually. Pay attention the amd64 versus my i386. Place on variable > sections > > Edit /etc/R/ldpahs place before if test -n... > : ${JAVA_HOME=/usr/lib/jvm/java-6-sun-1.6.0.24/jre} > : > ${R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/i386/server:${JAVA_HOME}/lib/i386:${JAVA_HOME}/../lib/i386:/usr/java/packages/lib/i386:/lib:/usr/lib} > > Again correct with your paths. > > And try to install rJava. > > Caveman > > > > On Fri, Mar 18, 2011 at 7:30 PM, jcheng liu <jcheng....@gmail.com> wrote: > >> Dear Orvalho Augusto, >> Thank so much for you response! >> We had run R CMD javareconf -e, and even R CMD javareconf in >> administrator. >> Actually, we had install the JDK. And in the output, only the item of JNI >> cpp flages could not be detected(I listed output below). What does the item >> mean? What need we install? >> >> Thanks, >> Jiacheng >> >> R CMD javareconf -e >> >> Java interpreter : /usr/bin/java >> Java version : 1.6.0_24 >> Java home path : /usr/java/jre1.6.0_24 >> Java compiler : /usr/bin/javac >> Java headers gen.: /usr/bin/javah >> Java archive tool: /usr/bin/jar >> Java library path: >> $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib >> JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server >> -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 >> -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm >> JNI cpp flags : >> >> The following Java variables have been exported: >> JAVA_HOME JAVA JAVAC JAVAH JAR JAVA_LIBS JAVA_CPPFLAGS >> JAVA_LD_LIBRARY_PATH >> Runnig: /bin/tcsh >> >> >> >> On 3/18/2011 12:53 PM, Orvalho Augusto wrote: >> >> Run >> R CMD javareconf -e >> >> as the being suggest by the output. That will try to guess where is Java. >> Or you can install the JDK_HOME and JAVA_HOME variables. >> >> Good luck. >> Caveman >> >> >> On Fri, Mar 18, 2011 at 4:39 PM, jcheng liu <jcheng....@gmail.com>wrote: >> >>> Dear all, >>> Installing rJava fails. The message was listed below. I wonder why cpp >>> flag >>> could not be detected, although I had installed. Thanks!!! >>> -Jiacheng >>> >>> R CMD INSTALL rJava_0.9-0.tar.gz >>> * installing to library >>> /data1/mri_researchers/wexler_data/jiacheng/R-2.12.0/library >>> * 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 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 : '/usr/bin/java' >>> archiver : '/usr/bin/jar' >>> compiler : '/usr/bin/javac' >>> header prep.: '/usr/bin/javah' >>> cpp flags : '' >>> java libs : '-L/usr/java/jre1.6.0_24/lib/amd64/server >>> -L/usr/java/jre1.6.0_24/lib/amd64 -L/usr/java/jre1.6.0_24/../lib/amd64 >>> -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib >>> -ljvm' >>> configure: error: One or more Java configuration variables are not set. >>> Make sure R is configured with full Java support (including JDK). Run >>> R CMD javareconf >>> as root to add Java support to R. >>> >>> If you don't have root privileges, run >>> R CMD javareconf -e >>> to set all Java-related variables and then install rJava. >>> >>> ERROR: configuration failed for package rJava >>> * removing /R-2.12.0/library/rJava >>> >>> [[alternative HTML version deleted]] >>> >>> >>> ______________________________________________ >>> 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. >>> >>> >> >> >> [[alternative HTML version deleted]]
______________________________________________ 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.