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.
