Dear Martin, SJava installation worked out fine. Thanks for all the help. Regards, Prashantha Hebbar Manipal Life Sciences Center India On Fri, Mar 18, 2011 at 10:55 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 03/18/2011 02:11 AM, MLSC MANIPAL wrote: > >> *Dear Sir, >> >> >> When I try to install "SJava", it is giving the following error:* >> >> Using R version 2.10.1, biocinstall version 2.5.11. >> Installing Bioconductor version 2.5 packages: >> [1] "SJava" >> Please wait... >> >> Warning in install.packages(pkgs = pkgs, repos = repos, ...) : >> argument 'lib' is missing: using '/usr/local/lib/R/site-library' >> trying URL ' >> >> http://www.bioconductor.org/packages/2.5/bioc/src/contrib/SJava_0.7 2.0.tar.gz >> ' >> Content type 'application/x-gzip' length 2210866 bytes (2.1 Mb) >> opened URL >> ================================================== >> downloaded 2.1 Mb >> >> * 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-openjdk/jre/../include' >> java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/i386/server >> -L/usr/lib/jvm/java-6-openjdk/jre/lib/i386 >> -L/usr/lib/jvm/java-6-openjdk/jre/../lib/i386 >> -L/usr/java/packages/lib/i386 >> -L/usr/lib/jni -L/lib -L/usr/lib -ljvm' >> Looking in /usr/lib/jvm/java-6-openjdk/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) >> > > The environment variable JAVA_HOME needs to be set, perhaps to > > /usr/lib/jvm/java > > Martin > > > 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/RtmpEiUbri/R.INSTALL327b23c6/SJava/inst:/tmp/RtmpEiUbri/R.INST ALL327b23c6/SJava/inst/org/omegahat/Jars/Environment.jar >> -o RForeignReference.h org.omegahat.R.Java.RForeignReference >> /usr/bin/javah -classpath >> >> /tmp/RtmpEiUbri/R.INSTALL327b23c6/SJava/inst:/tmp/RtmpEiUbri/R.INST ALL327b23c6/SJava/inst/org/omegahat/Jars/Environment.jar >> -o RManualFunctionActionListener.h >> org.omegahat.R.Java.RManualFunctionActionListener >> /usr/bin/javah -classpath >> >> /tmp/RtmpEiUbri/R.INSTALL327b23c6/SJava/inst:/tmp/RtmpEiUbri/R.INST ALL327b23c6/SJava/inst/org/omegahat/Jars/Environment.jar >> -o ROmegahatInterpreter.h org.omegahat.R.Java.ROmegahatInterpreter >> /usr/bin/javah -classpath >> >> /tmp/RtmpEiUbri/R.INSTALL327b23c6/SJava/inst:/tmp/RtmpEiUbri/R.INST ALL327b23c6/SJava/inst/org/omegahat/Jars/Environment.jar >> -o REvaluator.h org.omegahat.R.Java.REvaluator >> make -C RSJava >> make[1]: Entering directory >> `/tmp/RtmpEiUbri/R.INSTALL327b23c6/SJava/src/RSJava' >> /usr/bin/javah -classpath >> >> /tmp/RtmpEiUbri/R.INSTALL327b23c6/SJava/inst:/tmp/RtmpEiUbri/R.INST ALL327b23c6/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/RtmpEiUbri/R.INSTALL327b23c6/SJava/src/RSJava -I. >> -I/tmp/RtmpEiUbri/R.INSTALL327b23c6/SJava/inst/include >> -I/usr/lib/jvm/java-6-openjdk/jre/include >> -I/usr/lib/jvm/java-6-openjdk/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: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/RtmpEiUbri/R.INSTALL327b23c6/SJava/src/RSJava' >> make: *** [subdir] Error 2 >> ERROR: compilation failed for package ‘SJava’ >> * removing ‘/usr/local/lib/R/site-library/SJava’ >> >> The downloaded packages are in >> ‘/tmp/Rtmpy1rYnl/downloaded_packages’ >> Warning message: >> In install.packages(pkgs = pkgs, repos = repos, ...) : >> installation of package 'SJava' had non-zero exit status >> >> *Hence, Can you please suggest me a solution for this?* >> >> * * >> >> *Thanking you in anticipation.* >> >> * * >> >> *Regards,* >> *Rayan* >> >> [[alternative HTML version deleted]] >> >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor 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