Package: arji

Version: 0.3.16

Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD build arji

RetCode: 1

Time: 6.9 seconds

Status: ERROR

PackageFile: None

* checking for file 'arji/DESCRIPTION' ... OK
* preparing 'arji':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
installing R.css in E:/biocbld/bbs-2.1-bioc/tmpdir/Rinst537261798


---------- Making package arji ------------

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************

  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making arji.d from arji.c
gcc  -IC:/progra~1/java/jdk1.5.0_01/include -IC:/progra~1/java/jdk1.5.0_01/include/win32 -Ie:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c arji.c -o arji.o
arji.c:7:17: jni.h: No such file or directory
arji.c: In function `arji_destroyJavaVM':
arji.c:143: error: `JavaVM' undeclared (first use in this function)
arji.c:143: error: (Each undeclared identifier is reported only once
arji.c:143: error: for each function it appears in.)
arji.c:143: error: `thisjvm' undeclared (first use in this function)
arji.c:145: error: syntax error before ')' token
arji.c:146: error: syntax error before ')' token
arji.c: In function `arji_getJavaClass':
arji.c:156: error: `JNIEnv' undeclared (first use in this function)
arji.c:156: error: `env' undeclared (first use in this function)
arji.c:157: error: `jvm' undeclared (first use in this function)
arji.c:158: error: `jclass' undeclared (first use in this function)
arji.c:158: error: syntax error before "cls"
arji.c:160: error: `jmethodID' undeclared (first use in this function)
arji.c:160: error: syntax error before "mid"
arji.c:162: error: `jobjectArray' undeclared (first use in this function)
arji.c:163: error: `jstring' undeclared (first use in this function)
arji.c:166: error: syntax error before ')' token
arji.c:167: error: syntax error before ')' token
arji.c:168: error: `JNI_VERSION_1_4' undeclared (first use in this function)
arji.c:171: error: `cls' undeclared (first use in this function)
arji.c: In function `arji_getJavaStaticMethodID':
arji.c:187: error: syntax error before "cls"
arji.c:192: error: syntax error before ')' token
arji.c:193: error: syntax error before ')' token
arji.c:197: error: syntax error before ')' token
arji.c:198: error: syntax error before "R_ExternalPtrAddr"
arji.c:201: error: `mid' undeclared (first use in this function)
arji.c: In function `arji_getJavaNonstaticMethodID':
arji.c:216: error: syntax error before "cls"
arji.c:221: error: syntax error before ')' token
arji.c:222: error: syntax error before ')' token
arji.c:226: error: syntax error before ')' token
arji.c:227: error: syntax error before "R_ExternalPtrAddr"
arji.c: In function `arji_getJavaStaticFieldID':
arji.c:246: error: syntax error before "cls"
arji.c:247: error: `jfieldID' undeclared (first use in this function)
arji.c:250: error: syntax error before ')' token
arji.c:251: error: syntax error before ')' token
arji.c:255: error: syntax error before ')' token
arji.c:256: error: syntax error before "R_ExternalPtrAddr"
arji.c:265: error: `fid' undeclared (first use in this function)
arji.c: In function `arji_getJavaFieldID':
arji.c:281: error: syntax error before "cls"
arji.c:285: error: syntax error before ')' token
arji.c:286: error: syntax error before ')' token
arji.c:290: error: syntax error before ')' token
arji.c:291: error: syntax error before "R_ExternalPtrAddr"
arji.c: In function `arji_createJVM':
arji.c:315: error: `jint' undeclared (first use in this function)
arji.c:315: error: syntax error before "res"
arji.c:317: error: `JavaVMInitArgs' undeclared (first use in this function)
arji.c:317: error: syntax error before "vm_args"
arji.c:318: error: `JavaVMOption' undeclared (first use in this function)
arji.c:325: error: `options' undeclared (first use in this function)
arji.c:326: error: `vm_args' undeclared (first use in this function)
arji.c:329: error: `JNI_TRUE' undeclared (first use in this function)
arji.c:332: error: `res' undeclared (first use in this function)
arji.c:332: warning: implicit declaration of function `JNI_CreateJavaVM'
arji.c:316: warning: unused variable `JNIenvRef'
arji.c:316: warning: unused variable `JVMRef'
arji.c:316: warning: unused variable `outenv'
arji.c: In function `arji_callJNIArgable':
arji.c:351: error: `jvalue' undeclared (first use in this function)
arji.c:351: error: syntax error before "methodArgs"
arji.c:353: error: `jsize' undeclared (first use in this function)
arji.c:353: error: syntax error before "slen"
arji.c:354: error: `jchar' undeclared (first use in this function)
arji.c:354: error: `str' undeclared (first use in this function)
arji.c:355: error: syntax error before "jstr"
arji.c:357: error: `jobject' undeclared (first use in this function)
arji.c:376: error: syntax error before ')' token
arji.c:377: error: syntax error before ')' token
arji.c:378: error: syntax error before "R_ExternalPtrAddr"
arji.c:379: error: syntax error before "R_ExternalPtrAddr"
arji.c:385: error: syntax error before ')' token
arji.c:386: error: `obj' undeclared (first use in this function)
arji.c:386: error: syntax error before "R_ExternalPtrAddr"
arji.c:390: error: syntax error before ')' token
arji.c:391: error: syntax error before ')' token
arji.c:404: error: `methodArgs' undeclared (first use in this function)
arji.c:404: error: `jdouble' undeclared (first use in this function)
arji.c:404: error: syntax error before "REAL"
arji.c:405: error: syntax error before "else"
arji.c:407: error: `ja' undeclared (first use in this function)
arji.c:412: error: case label not within a switch statement
arji.c:416: error: `jboolean' undeclared (first use in this function)
arji.c:416: error: syntax error before "LOGICAL"
arji.c:417: error: syntax error before "else"
arji.c:419: error: `jbooleanArray' undeclared (first use in this function)
arji.c:421: error: syntax error before ')' token
arji.c:424: error: syntax error before "else"
arji.c:425: error: break statement not within loop or switch
arji.c:426: error: case label not within a switch statement
arji.c:429: error: `jint' undeclared (first use in this function)
arji.c:429: error: syntax error before "INTEGER"
arji.c:430: error: syntax error before "else"
arji.c:435: warning: no return statement in function returning non-void
arji.c: At top level:
arji.c:436: error: syntax error before "break"
arji.c:440: error: syntax error before '.' token
arji.c:449: error: syntax error before '.' token
arji.c:459: error: syntax error before '->' token
arji.c:459: error: syntax error before string constant
arji.c:459: warning: type defaults to `int' in declaration of `Rf_error'
arji.c:459: error: conflicting types for 'Rf_error'
e:/biocbld/bbs-2.1-bioc/R/include/R_ext/Error.h:28: error: previous declaration of 'Rf_error' was here
arji.c:459: warning: data definition has no type or storage class
arji.c:465: error: syntax error before '->' token
arji.c:465: error: syntax error before string constant
arji.c:465: warning: type defaults to `int' in declaration of `Rf_error'
arji.c:465: warning: data definition has no type or storage class
arji.c:470: error: syntax error before '->' token
arji.c:470: error: syntax error before string constant
arji.c:470: warning: type defaults to `int' in declaration of `Rf_error'
arji.c:470: warning: data definition has no type or storage class
arji.c:471: warning: type defaults to `int' in declaration of `slen'
arji.c:471: confused by earlier errors, bailing out
make[3]: *** [arji.o] Error 1
make[2]: *** [srcDynlib] Error 2
make[1]: *** [all] Error 2
make: *** [pkg-arji] Error 2
*** Installation of arji failed ***

Removing 'E:/biocbld/bbs-2.1-bioc/tmpdir/Rinst537261798/arji'
 ERROR
Installation failed.
Removing 'E:/biocbld/bbs-2.1-bioc/tmpdir/Rinst537261798'