[BioC] Failed installing SJava on MacOS and Linux!
Michael Dondrup
Michael.Dondrup at uni.no
Wed Jan 20 17:26:53 CET 2010
Thank you Cristobal and Martin,
this is now working for me on ubuntu 9.04, your hints were correct!
In summary, here are the two commands I used:
> sudo JAVA_HOME=/usr/lib/jvm/java-6-sun/ R CMD INSTALL -c SJava_0.73.0.tar.gz
(maybe there was a change in the path layout between java 5 and 6?)
....
** R
** inst
cp: cannot overwrite directory `/usr/local/lib/R/site-library/SJava/libs' with non-directory
( > this does not seem to have any effect )
sh: /bin/tarxf: not found ( > probably meant "/bin/tar xf" ? )
** preparing package for lazy loading
Creating a new generic function for "merge" in "SJava"
** help
......
then:
> export $LD_LIBRARY_PATH=/usr/lib/jvm/java-6-sun/jre/lib/i386/client/
( this should maybe be automatic ?)
> R
> library(SJava)
Load the Java VM with .JavaInit()
> .JavaInit()
> example(.Java)
So, problem partially solved, thank you again
Am Jan 20, 2010 um 3:58 PM schrieb Cristobal Fresno Rodríguez:
> Hi Michael,
> I have Ubuntu 9.10 and could install SJava doing the folowing:
>
> 1) The problem you have is on the JAVA_HOME variable as it can't find jni.h. due to the R java conf.
> Were it says "Looking in /usr/lib/jvm/java-6-sun-1.6.0.16/jre/include" should say "/usr/lib/jvm/java-6-sun-1.6.0.16/include". So you got the exception of java and the missing jni.h.
> On my configuration
> $sudo find / -name jni.h
> /usr/lib/jvm/java-6-sun-1.6.0.15/include/jni.h
> then set the JAVA_HOME
> $ export JAVA_HOME=/usr/lib/jvm/java-6-sun-1.6.0.15
> $ $JAVA_HOME
> bash: /usr/lib/jvm/java-6-sun-1.6.0.15: is a directory
>
> 2) Download SJava, untar and install with R
> $R CMD INSTALL SJava
> bla bla bla ...
> ** R
> ** inst
> cp: cannot overwrite directory `/usr/local/lib/R/library/SJava/libs' with non-directory
> sh: /bin/tarxf: not found
> ** preparing package for lazy loading
> Creating a new generic function for "merge" in "SJava"
> ** help
> *** installing help indices
> ** building package indices ...
> * DONE (SJava)
>
> 3) Try to run SJava with no luck
> $R
> > library(SJava)
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared library '/usr/local/lib/R/library/SJava/libs/SJava.so':
> libjvm.so: cannot open shared object file: No such file or directory
> Error in library(SJava) : .First.lib failed for 'SJava'
>
> Now we are missing libjvm.so. Even if I set on the PATH variable or a symbolic link form SJava/libs directory, can't get it work.
> $ sudo find / -name libjvm.so
> /usr/lib/jvm/java-6-openjdk/jre/lib/i386/client/libjvm.so
> /usr/lib/jvm/java-6-openjdk/jre/lib/i386/cacao/libjvm.so
> /usr/lib/jvm/java-6-openjdk/jre/lib/i386/server/libjvm.so
> /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/i386/client/libjvm.so
> /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/i386/server/libjvm.so
>
> the work around I found I to load the library before calling SJava. Someone else, may improve it.
> $R
> > dyn.load("/usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/i386/client/libjvm.so")
> > library(SJava)
> Load the Java VM with .JavaInit()
> >
>
> Hope it works for you too,
> Kachelo
>
> 2010/1/20 Michael Dondrup <Michael.Dondrup at uni.no>
> Hi,
> I thought I could do a quick test on Ubuntu in my virtual box and compare, but that went even worse. I started on a
> freshly installed R 2.10.1 (from CRAN) in ubuntu 9.04. Here are the details, any ideas?
>
> michi at michi-laptop:~$ sudo R CMD javareconf
> Java interpreter : /usr/bin/java
> Java version : 1.6.0_16
> Java home path : /usr/lib/jvm/java-6-sun-1.6.0.16/jre
> Java compiler : /usr/bin/javac
> Java headers gen.: /usr/bin/javah
> Java archive tool: /usr/bin/jar
> Java library path: $(JAVA_HOME)/lib/i386/client:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386::/usr/java/packages/lib/i386:/lib:/usr/lib
> JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -L$(JAVA_HOME)/lib/i386 -L$(JAVA_HOME)/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm
> JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
>
> Updating Java configuration in /etc/R
> Done.
>
> michi at michi-laptop:~$ sudo R CMD INSTALL -c Desktop/SJava_0.73.0.tar.gz
> * installing to library ‘/usr/local/lib/R/site-library’
> * installing *source* package ‘SJava’ ...
> checking shlib support in R... 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/usr/lib/jvm/java-6-sun-1.6.0.16/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.16/jre/../include/linux'
> java libs : '-L/usr/lib/jvm/java-6-sun-1.6.0.16/jre/lib/i386/client -L/usr/lib/jvm/java-6-sun-1.6.0.16/jre/lib/i386 -L/usr/lib/jvm/java-6-sun-1.6.0.16/jre/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm'
> Looking in /usr/lib/jvm/java-6-sun-1.6.0.16/jre/include
> Exception in thread "main" java.lang.NullPointerException
> at jniParameters.findJniInclude(jniParameters.java:76)
> at jniParameters.findJniInclude(jniParameters.java:61)
> at jniParameters.compute(jniParameters.java:40)
> at jniParameters.<init>(jniParameters.java:12)
> at jniBashParameters.<init>(jniBashParameters.java:11)
> at jniBashParameters.main(jniBashParameters.java:7)
> checking for gcc... gcc
> 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 accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking for Rf_initEmbeddedR in -lR... yes
> configure: creating ./config.status
> config.status: creating Makevars
> config.status: creating src/Makevars
> config.status: creating src/RSJava/Makefile
> config.status: creating inst/scripts/RJava.bsh
> config.status: creating inst/scripts/RJava.csh
> config.status: creating cleanup
> config.status: creating inst/scripts/RJava
> Copying the cleanup script to the scripts/ directory
> ** libs
> /usr/bin/javah -classpath /tmp/RtmpkgwAO7/R.INSTALL327b23c6/SJava/inst:/tmp/RtmpkgwAO7/R.INSTALL327b23c6/SJava/inst/org/omegahat/Jars/Environment.jar -o RForeignReference.h org.omegahat.R.Java.RForeignReference
> /usr/bin/javah -classpath /tmp/RtmpkgwAO7/R.INSTALL327b23c6/SJava/inst:/tmp/RtmpkgwAO7/R.INSTALL327b23c6/SJava/inst/org/omegahat/Jars/Environment.jar -o RManualFunctionActionListener.h org.omegahat.R.Java.RManualFunctionActionListener
> /usr/bin/javah -classpath /tmp/RtmpkgwAO7/R.INSTALL327b23c6/SJava/inst:/tmp/RtmpkgwAO7/R.INSTALL327b23c6/SJava/inst/org/omegahat/Jars/Environment.jar -o ROmegahatInterpreter.h org.omegahat.R.Java.ROmegahatInterpreter
> /usr/bin/javah -classpath /tmp/RtmpkgwAO7/R.INSTALL327b23c6/SJava/inst:/tmp/RtmpkgwAO7/R.INSTALL327b23c6/SJava/inst/org/omegahat/Jars/Environment.jar -o REvaluator.h org.omegahat.R.Java.REvaluator
> make -C RSJava
> make[1]: Entering directory `/tmp/RtmpkgwAO7/R.INSTALL327b23c6/SJava/src/RSJava'
> /usr/bin/javah -classpath /tmp/RtmpkgwAO7/R.INSTALL327b23c6/SJava/inst:/tmp/RtmpkgwAO7/R.INSTALL327b23c6/SJava/inst/org/omegahat/Jars/Environment.jar -o OmegaInterfaceManager.h \
> org.omegahat.Interfaces.NativeInterface.OmegaInterfaceManager
> gcc -std=gnu99 -I/usr/share/R/include -D_R_ -I/usr/lib/R/include -I/usr/lib/R/include/R_ext -I/tmp/RtmpkgwAO7/R.INSTALL327b23c6/SJava/src/RSJava -I. -I/tmp/RtmpkgwAO7/R.INSTALL327b23c6/SJava/inst/include -I/usr/lib/jvm/java-6-sun-1.6.0.16/jre/include -I/usr/lib/jvm/java-6-sun-1.6.0.16/jre/include/ -fpic -g -O2 -c CtoJava.c -o CtoJava.o
> In file included from CtoJava.c:6:
> CtoJava.h:9:17: error: jni.h: No such file or directory
> In file included from CtoJava.c:6:
> CtoJava.h:14: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘NullObject’
> CtoJava.h:17: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘OmegahatInterfaceManagerClass’
> CtoJava.h:18: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘BasicClassValueAccessors’
> CtoJava.h:100: error: expected declaration specifiers or ‘...’ before ‘jboolean’
> CtoJava.h:106: error: expected ‘)’ before ‘Manager’
> CtoJava.h:109: error: expected ‘)’ before ‘*’ token
> CtoJava.h:112: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_createForeignReference’
> CtoJava.h:116: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘getInterfaceManager’
> CtoJava.h:117: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘setInterfaceManager’
> CtoJava.h:120: error: expected declaration specifiers or ‘...’ before ‘JNIEnv’
> CtoJava.h:123: error: expected declaration specifiers or ‘...’ before ‘jboolean’
> CtoJava.h:123: error: expected declaration specifiers or ‘...’ before ‘jboolean’
> CtoJava.h:123: error: expected declaration specifiers or ‘...’ before ‘jboolean’
> CtoJava.h:126: error: expected ‘)’ before ‘*’ token
> CtoJava.h:129: error: expected ‘)’ before ‘*’ token
> CtoJava.h:137: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘findGetPrimitiveMethodID’
> CtoJava.h:140: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> CtoJava.h:142: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> CtoJava.h:143: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> CtoJava.h:144: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> CtoJava.h:145: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘releaseThreadJNIEnv’
> CtoJava.h:149: error: expected ‘)’ before ‘*’ token
> CtoJava.h:150: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> In file included from CtoJava.c:8:
> ErrorHandling.h:14: error: expected declaration specifiers or ‘...’ before ‘JNIEnv’
> ErrorHandling.h:19: error: expected declaration specifiers or ‘...’ before ‘JNIEnv’
> ErrorHandling.h:20: error: expected ‘)’ before ‘*’ token
> ErrorHandling.h:21: error: expected ‘)’ before ‘*’ token
> ErrorHandling.h:24: error: expected declaration specifiers or ‘...’ before ‘jthrowable’
> ErrorHandling.h:24: error: expected declaration specifiers or ‘...’ before ‘JNIEnv’
> ErrorHandling.h:27: error: expected ‘)’ before ‘*’ token
> ErrorHandling.h:30: error: expected declaration specifiers or ‘...’ before ‘JNIEnv’
> In file included from CtoJava.c:9:
> JNIUtils.h:12: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘get_method_id’
> JNIUtils.h:16: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘get_object_class_name’
> JNIUtils.h:19: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘get_java_class_name’
> JNIUtils.h:23: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘VMNewStringArray’
> JNIUtils.h:26: error: expected ‘)’ before ‘obj’
> In file included from CtoJava.c:13:
> ManagerInterfaceUtils.h:12: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘callGenericOmegaMethod’
> ManagerInterfaceUtils.h:18: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘callConstructorMethod’
> ManagerInterfaceUtils.h:22: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘evalOmegaExpression’
> ManagerInterfaceUtils.h:27: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘get_object_datatype’
> ManagerInterfaceUtils.h:31: error: expected ‘)’ before ‘OmegahatInterfaceManagerClass’
> ManagerInterfaceUtils.h:35: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘getOmegahatReferenceValue’
> In file included from CtoJava.c:14:
> OmegaInterfaceManager.h:17: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘jboolean’
> CtoJava.c:17: error: expected ‘)’ before ‘*’ token
> CtoJava.c:25: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> CtoJava.c:38: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘vm1_args’
> CtoJava.c:39: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘vm2_args’
> CtoJava.c:41: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> CtoJava.c:47: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘interfaceManager’
> CtoJava.c:63: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> CtoJava.c:70: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘doubleValueID’
> CtoJava.c:73: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘BasicClassValueAccessors’
> CtoJava.c:76: error: expected ‘)’ before ‘Manager’
> CtoJava.c:79: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘OmegahatInterfaceManagerClass’
> CtoJava.c:80: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘BasicClassValueAccessors’
> CtoJava.c:83: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘NullObject’
> CtoJava.c:89: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘MetaForeignReferenceClass’
> CtoJava.c:94: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘MetaForeignReferenceConstructorId’
> CtoJava.c:96: error: expected ‘)’ before ‘*’ token
> CtoJava.c:101: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘arrayClasses’
> CtoJava.c:119: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘wrapperClasses’
> CtoJava.c:120: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘wrapperConstructor’
> CtoJava.c: In function ‘interface_start_VM’:
> CtoJava.c:164: error: too many arguments to function ‘create_Java_vm’
> CtoJava.c: At top level:
> CtoJava.c:182: error: expected declaration specifiers or ‘...’ before ‘jboolean’
> CtoJava.c: In function ‘create_Java_vm’:
> CtoJava.c:184: error: ‘jint’ undeclared (first use in this function)
> CtoJava.c:184: error: (Each undeclared identifier is reported only once
> CtoJava.c:184: error: for each function it appears in.)
> CtoJava.c:184: error: expected ‘;’ before ‘res’
> CtoJava.c:187: error: ‘std_env’ undeclared (first use in this function)
> CtoJava.c:189: error: ‘jvm’ undeclared (first use in this function)
> CtoJava.c:204: error: ‘vm_args’ undeclared (first use in this function)
> CtoJava.c:204: error: ‘JDK1_1InitArgs’ undeclared (first use in this function)
> CtoJava.c:204: error: expected expression before ‘)’ token
> CtoJava.c:210: error: expected expression before ‘)’ token
> CtoJava.c:210: error: ‘vm1_args’ undeclared (first use in this function)
> CtoJava.c:211: error: ‘JNI_VERSION_1_1’ undeclared (first use in this function)
> CtoJava.c:213: warning: implicit declaration of function ‘JNI_GetDefaultJavaVMInitArgs’
> CtoJava.c: At top level:
> CtoJava.c:283: warning: data definition has no type or storage class
> CtoJava.c:283: warning: type defaults to ‘int’ in declaration of ‘tmp’
> CtoJava.c:283: error: ‘user_classpath’ undeclared here (not in a function)
> CtoJava.c:283: error: ‘vm_args’ undeclared here (not in a function)
> CtoJava.c:283: warning: initialization makes integer from pointer without a cast
> CtoJava.c:283: error: initializer element is not constant
> CtoJava.c:285: warning: data definition has no type or storage class
> CtoJava.c:285: warning: type defaults to ‘int’ in declaration of ‘strcpy’
> CtoJava.c:285: warning: parameter names (without types) in function declaration
> CtoJava.c:285: error: conflicting types for ‘strcpy’
> CtoJava.c:286: error: expected ‘)’ before string constant
> CtoJava.c:287: error: expected ‘)’ before ‘->’ token
> CtoJava.c:288: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘->’ token
> CtoJava.c:291: error: expected identifier or ‘(’ before ‘if’
> CtoJava.c:298: error: expected identifier or ‘(’ before ‘if’
> CtoJava.c:305: error: expected identifier or ‘(’ before ‘return’
> CtoJava.c:306: error: expected identifier or ‘(’ before ‘}’ token
> CtoJava.c: In function ‘exists_Java_vm’:
> CtoJava.c:311: error: ‘std_env’ undeclared (first use in this function)
> CtoJava.c: At top level:
> CtoJava.c:316: error: expected ‘)’ before ‘Manager’
> CtoJava.c:354: error: expected ‘)’ before ‘Manager’
> CtoJava.c:475: error: expected ‘)’ before ‘*’ token
> CtoJava.c:517: error: expected declaration specifiers or ‘...’ before ‘JNIEnv’
> CtoJava.c: In function ‘whatJavaType’:
> CtoJava.c:518: error: ‘jobject’ undeclared (first use in this function)
> CtoJava.c:518: error: expected ‘;’ before ‘obj’
> CtoJava.c:519: error: ‘obj’ undeclared (first use in this function)
> CtoJava.c:519: error: expected ‘;’ before ‘javaObject’
> CtoJava.c:526: error: ‘env’ undeclared (first use in this function)
> CtoJava.c:526: error: ‘arrayClasses’ undeclared (first use in this function)
> CtoJava.c:526: error: ‘JNI_TRUE’ undeclared (first use in this function)
> CtoJava.c:530: error: ‘primitiveClasses’ undeclared (first use in this function)
> CtoJava.c: At top level:
> CtoJava.c:552: error: expected declaration specifiers or ‘...’ before ‘jboolean’
> CtoJava.c:553: error: expected declaration specifiers or ‘...’ before ‘jboolean’
> CtoJava.c:553: error: expected declaration specifiers or ‘...’ before ‘jboolean’
> CtoJava.c: In function ‘which_java_type’:
> CtoJava.c:562: error: ‘builtIn’ undeclared (first use in this function)
> CtoJava.c:563: error: ‘JNI_TRUE’ undeclared (first use in this function)
> CtoJava.c:566: error: ‘JNI_FALSE’ undeclared (first use in this function)
> CtoJava.c: At top level:
> CtoJava.c:708: error: expected ‘)’ before ‘*’ token
> CtoJava.c:866: error: expected ‘)’ before ‘*’ token
> CtoJava.c:1047: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> CtoJava.c:1074: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> CtoJava.c:1081: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> CtoJava.c:1132: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘releaseThreadJNIEnv’
> CtoJava.c:1152: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> CtoJava.c:1159: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> CtoJava.c:1166: error: expected ‘)’ before ‘*’ token
> CtoJava.c: In function ‘RS_JAVA_terminateJava’:
> CtoJava.c:1174: error: ‘JavaVM’ undeclared (first use in this function)
> CtoJava.c:1174: error: ‘vm’ undeclared (first use in this function)
> CtoJava.c:1174: warning: implicit declaration of function ‘getJavaVM’
> CtoJava.c:1177: error: ‘jvm’ undeclared (first use in this function)
> CtoJava.c: At top level:
> CtoJava.c:1184: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘getInterfaceManager’
> CtoJava.c:1188: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘setInterfaceManager’
> CtoJava.c:1202: error: expected ‘)’ before ‘*’ token
> CtoJava.c:1225: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_createForeignReference’
> CtoJava.c:1243: error: expected ‘)’ before ‘*’ token
> CtoJava.c:1292: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘findGetPrimitiveMethodID’
> make[1]: *** [CtoJava.o] Error 1
> make[1]: Leaving directory `/tmp/RtmpkgwAO7/R.INSTALL327b23c6/SJava/src/RSJava'
> make: *** [subdir] Error 2
> ERROR: compilation failed for package ‘SJava’
> * removing ‘/usr/local/lib/R/site-library/SJava’
> michi at michi-laptop:~$
>
> -----------------------------------------------------------------------------------------------------------------------
> > sessionInfo()
> R version 2.10.1 (2009-12-14)
> i486-pc-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
> >
> -----------------------------------------------------------------------------------------------------------------------
> michi at michi-laptop:~$ java -version
> java version "1.6.0_16"
> Java(TM) SE Runtime Environment (build 1.6.0_16-b01)
> Java HotSpot(TM) Client VM (build 14.2-b01, mixed mode, sharing)
>
> -----------------------------------------------------------------------------------------------------------------------
> michi at michi-laptop:~$ uname -a
> Linux michi-laptop 2.6.28-17-generic #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 i686 GNU/Linux
>
>
> Thanx again for reading that far ;)
>
> Am Jan 19, 2010 um 6:37 PM schrieb Seth Falcon:
>
> > On 1/19/10 8:58 AM, Martin Morgan wrote:
> >> Michael Dondrup wrote:
> >>> Am Jan 19, 2010 um 3:39 PM schrieb Martin Morgan:
> >>>
> >>>> Michael Dondrup wrote:
> >>>>> Hi,
> >>>>> I would like to use RWebServices and therefore SJava on Mac OS snow leopard. The documentation does not explicitly mention Mac os, so it's
> >>>>> maybe not supported, but i hope it can be made working anyway.
> >>>>> Maybe somebody out there got this configuration running and could help? I am trying to install SJava 0.72. I try the following:
> >>>>>
> >>>>>> library(SJava)
> >>>>> Load the Java VM with .JavaInit()
> >>>>>> .JavaInit()
> >>>>>> example(.Java)
> >>>>> .Java> v<- .JavaConstructor("java.util.Vector", as.integer(10))
> >>>>>
> >>>>> .Java> .Java(v, "add", "A string element")
> >>>>> Error in .Java(v, "add", "A string element") :
> >>>>> Can't find org.omegahat.R.Java.RForeignReference
> >>
> >> this is in org.omegahat/Jars/RJava.jar, e.g.,
> >>
> >> jar tf org.omegahat/Jars/RJava.jar
> >>
> >
> > Curious, as this jar did not appear on your classpath in your previous mail.
> >
> > I'm able to reproduce the error on my Snow Leopard laptop. I also notice that I don't have this jar. There are .class files under the package structure in org/omegahat/R/Java/*.class. RForeignReference.class is among them and this would seem to be the purpose of the "<...>/SJava/org/.." entry in class path.
> >
> [snip]
>
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