* checking for file 'arji/DESCRIPTION' ... OK
* preparing 'arji':
* checking DESCRIPTION meta-information ... OK
* cleaning src
Makefile:1: Makevars: No such file or directory
make: *** No rule to make target `Makevars'. Stop.
* installing the package to re-build vignettes
* Installing *source* package 'arji' ...
configure: creating ./config.status
config.status: creating src/Makevars
** libs
** arch -
/usr/lib/jvm/jre/bin/javac ../inst/java/*.java
/loc/biocbuild/1.9d/R/bin/R CMD SHLIB arji.c
make[1]: Entering directory `/loc/biocbuild/1.9d/Rpacks/arji/src'
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/lib/jvm/jre/include -I/usr/lib/jvm/jre/include/linux -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c arji.c -o arji.o
arji.c: In function `arji_destroyJavaVM':
arji.c:144: warning: unused variable `kill'
arji.c: In function `arji_getJavaClass':
arji.c:168: warning: dereferencing type-punned pointer will break strict-aliasing rules
arji.c:160: warning: unused variable `mid'
arji.c:161: warning: unused variable `stringClass'
arji.c:162: warning: unused variable `args'
arji.c:163: warning: unused variable `jstr'
arji.c: In function `arji_getJavaStaticMethodID':
arji.c:194: warning: dereferencing type-punned pointer will break strict-aliasing rules
arji.c: In function `arji_getJavaNonstaticMethodID':
arji.c:223: warning: dereferencing type-punned pointer will break strict-aliasing rules
arji.c: In function `arji_getJavaStaticFieldID':
arji.c:252: warning: dereferencing type-punned pointer will break strict-aliasing rules
arji.c: In function `arji_getJavaFieldID':
arji.c:287: warning: dereferencing type-punned pointer will break strict-aliasing rules
arji.c: In function `arji_createJVM':
arji.c:328: warning: dereferencing type-punned pointer will break strict-aliasing rules
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:388: warning: dereferencing type-punned pointer will break strict-aliasing rules
arji.c:612: warning: unsigned int format, jobject arg (arg 2)
arji.c:613: warning: unsigned int format, pointer arg (arg 2)
arji.c: In function `arji_getJavaStaticField':
arji.c:674: warning: dereferencing type-punned pointer will break strict-aliasing rules
arji.c: In function `arji_getJavaField':
arji.c:843: warning: dereferencing type-punned pointer will break strict-aliasing rules
arji.c:834: warning: unused variable `cls'
arji.c: In function `convertJavaString':
arji.c:1017: warning: dereferencing type-punned pointer will break strict-aliasing rules
arji.c:1026: warning: unsigned int format, pointer arg (arg 2)
arji.c:1027: warning: unsigned int format, pointer arg (arg 2)
arji.c: In function `convertJavaObject':
arji.c:1063: warning: unsigned int format, pointer arg (arg 2)
arji.c:1071: warning: control reaches end of non-void function
arji.c: In function `arji_getJavaField':
arji.c:997: warning: control reaches end of non-void function
arji.c: In function `arji_getJavaStaticField':
arji.c:828: warning: control reaches end of non-void function
arji.c: In function `arji_callJNIArgable':
arji.c:353: warning: `obj' might be used uninitialized in this function
arji.c: At top level:
arji.c:66: warning: `JavaMethod_type_tag' defined but not used
gcc -shared -L/usr/local/lib64 -o arji.so arji.o -L/usr/lib/jvm/jre/jre/lib/amd64 -L/usr/lib/jvm/jre/jre/lib/i386 -ljava -L/usr/lib/jvm/jre/jre/lib/amd64/server -L/usr/lib/jvm/jre/jre/lib/i386/client -ljvm
make[1]: Leaving directory `/loc/biocbuild/1.9d/Rpacks/arji/src'
** R
** inst
** help
>>> Building/Updating help pages for package 'arji'
Formats: text html latex example
JavaVMRef-class text html latex example
createJVM text html latex example
reflect text html latex example
** building package indices ...
* DONE (arji)
* creating vignettes ... ERROR
Warning message:
A live JVM is already present in: createJVM(opts = paste("-Djava.class.path=", system.file("java",
Error: chunk 6 (label=lkdemo)
Error in jvmptr(jvmref) : no direct or inherited method for function 'jvmptr' for this call
Error in buildVignettes(dir = ".") : Error: chunk 6 (label=lkdemo)
Error in jvmptr(jvmref) : no direct or inherited method for function 'jvmptr' for this call
Execution halted