[BioC] error while installing SJava

[Martin Morgan]

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_0.72.0.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.INSTALL327b23c6/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.INSTALL327b23c6/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.INSTALL327b23c6/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.INSTALL327b23c6/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.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/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]]
>
>
>
>
> _______________________________________________
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