SJava 0.88.0
Martin Morgan
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/SJava | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | N O T S U P P O R T E D |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SJava/DESCRIPTION’ ... OK
* this is package ‘SJava’ version ‘0.88.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SJava’ can be installed ... [13s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘SJava/R/zzz.R’:
.onLoad calls:
packageStartupMessage("Load the Java VM with .JavaInit()")
See section ‘Good practice’ in '?.onAttach'.
defaultJavaPath: no visible global function definition for ‘getenv’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/SJava/libs/SJava.so’:
Found non-API calls to R: ‘R_CStackLimit’, ‘R_Interactive’,
‘Rf_endEmbeddedR’, ‘Rf_initialize_R’, ‘run_Rmainloop’,
‘setup_Rmainloop’
File ‘/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/SJava/libs/libRInterpreter.so’:
Found non-API calls to R: ‘R_CStackLimit’, ‘R_Interactive’,
‘Rf_endEmbeddedR’, ‘Rf_initialize_R’, ‘run_Rmainloop’,
‘setup_Rmainloop’
File ‘/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/SJava/libs/libSJava.so’:
Found non-API calls to R: ‘R_CStackLimit’, ‘R_Interactive’,
‘Rf_endEmbeddedR’, ‘Rf_initialize_R’, ‘run_Rmainloop’,
‘setup_Rmainloop’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... [2s/2s] OK
* checking PDF version of manual ... OK
NOTE: There were 4 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00check.log’
for details.
* 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-amd64/jre/../include'
java libs : '-L/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/server -ljvm'
Looking in /usr/lib/jvm/java-6-openjdk-amd64/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 /home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/Environment.jar -o RForeignReference.h org.omegahat.R.Java.RForeignReference
/usr/bin/javah -classpath /home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/Environment.jar -o RManualFunctionActionListener.h org.omegahat.R.Java.RManualFunctionActionListener
/usr/bin/javah -classpath /home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/Environment.jar -o ROmegahatInterpreter.h org.omegahat.R.Java.ROmegahatInterpreter
/usr/bin/javah -classpath /home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/Environment.jar -o REvaluator.h org.omegahat.R.Java.REvaluator
make -C RSJava
make[1]: Entering directory `/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava'
/usr/bin/javah -classpath /home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/Environment.jar -o OmegaInterfaceManager.h \
org.omegahat.Interfaces.NativeInterface.OmegaInterfaceManager
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -fpic -g -O2 -Wall -c CtoJava.c -o CtoJava.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -fpic -g -O2 -Wall -c ErrorHandling.c -o ErrorHandling.o
ErrorHandling.c: In function ‘throw_Java_exception’:
ErrorHandling.c:51:2: warning: implicit declaration of function ‘REprintf’ [-Wimplicit-function-declaration]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -fpic -g -O2 -Wall -c ManagerInterfaceUtils.c -o ManagerInterfaceUtils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -fpic -g -O2 -Wall -c References.c -o References.o
References.c: In function ‘initReferenceClasses’:
References.c:100:6: warning: implicit declaration of function ‘REprintf’ [-Wimplicit-function-declaration]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -fpic -g -O2 -Wall -c JNIUtils.c -o JNIUtils.o
JNIUtils.c: In function ‘get_java_class_name’:
JNIUtils.c:78:6: warning: implicit declaration of function ‘REprintf’ [-Wimplicit-function-declaration]
cp CtoJava.h ErrorHandling.h ManagerInterfaceUtils.h References.h JNIUtils.h /home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include
make[1]: Leaving directory `/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c ConverterExamples.c -o ConverterExamples.o
ConverterExamples.c: In function ‘RS_JAVA_toJavaFunctionConverter’:
ConverterExamples.c:249:18: warning: variable ‘fun’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c Converters.c -o Converters.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c Reflectance.c -o Reflectance.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c REmbed.c -o REmbed.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c REmbedWin.c -o REmbedWin.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c REval.c -o REval.o
REval.c: In function ‘sjava_tryEval’:
REval.c:55:9: warning: passing argument 2 of ‘Rf_eval’ from incompatible pointer type [enabled by default]
/home/biocbuild/bbs-2.13-bioc/R/include/Rinternals.h:671:6: note: expected ‘SEXP’ but argument is of type ‘const struct JNINativeInterface_ **’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RFunctionListener.c -o RFunctionListener.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RReferenceCall.c -o RReferenceCall.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RStoJava.c -o RStoJava.o
RStoJava.c: In function ‘s_register_VM’:
RStoJava.c:360:17: warning: variable ‘msg’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RtoJava.c -o RtoJava.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RSJava/CtoJava.c -o RSJava/CtoJava.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RSJava/ErrorHandling.c -o RSJava/ErrorHandling.o
RSJava/ErrorHandling.c: In function ‘throw_Java_exception’:
RSJava/ErrorHandling.c:51:2: warning: implicit declaration of function ‘REprintf’ [-Wimplicit-function-declaration]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RSJava/ManagerInterfaceUtils.c -o RSJava/ManagerInterfaceUtils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RSJava/References.c -o RSJava/References.o
RSJava/References.c: In function ‘initReferenceClasses’:
RSJava/References.c:100:6: warning: implicit declaration of function ‘REprintf’ [-Wimplicit-function-declaration]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RSJava/JNIUtils.c -o RSJava/JNIUtils.o
RSJava/JNIUtils.c: In function ‘get_java_class_name’:
RSJava/JNIUtils.c:78:6: warning: implicit declaration of function ‘REprintf’ [-Wimplicit-function-declaration]
gcc -std=gnu99 -shared -L/usr/local/lib -o SJava.so ConverterExamples.o Converters.o Reflectance.o REmbed.o REmbedWin.o REval.o RFunctionListener.o RReferenceCall.o RStoJava.o RtoJava.o RSJava/CtoJava.o RSJava/ErrorHandling.o RSJava/ManagerInterfaceUtils.o RSJava/References.o RSJava/JNIUtils.o -L/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/server -ljvm -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
mkdir -p /home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/SJava/libs
ln -s SJava.so /home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/SJava/libs/libSJava.so
ln -s SJava.so /home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/SJava/libs/libRInterpreter.so
make -C RSJava
make[1]: Entering directory `/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -fpic -g -O2 -Wall -c CtoJava.c -o CtoJava.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -fpic -g -O2 -Wall -c ErrorHandling.c -o ErrorHandling.o
ErrorHandling.c: In function ‘throw_Java_exception’:
ErrorHandling.c:51:2: warning: implicit declaration of function ‘REprintf’ [-Wimplicit-function-declaration]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -fpic -g -O2 -Wall -c ManagerInterfaceUtils.c -o ManagerInterfaceUtils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -fpic -g -O2 -Wall -c References.c -o References.o
References.c: In function ‘initReferenceClasses’:
References.c:100:6: warning: implicit declaration of function ‘REprintf’ [-Wimplicit-function-declaration]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -fpic -g -O2 -Wall -c JNIUtils.c -o JNIUtils.o
JNIUtils.c: In function ‘get_java_class_name’:
JNIUtils.c:78:6: warning: implicit declaration of function ‘REprintf’ [-Wimplicit-function-declaration]
cp CtoJava.h ErrorHandling.h ManagerInterfaceUtils.h References.h JNIUtils.h /home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include
make[1]: Leaving directory `/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c ConverterExamples.c -o ConverterExamples.o
ConverterExamples.c: In function ‘RS_JAVA_toJavaFunctionConverter’:
ConverterExamples.c:249:18: warning: variable ‘fun’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c Converters.c -o Converters.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c Reflectance.c -o Reflectance.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c REmbed.c -o REmbed.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c REmbedWin.c -o REmbedWin.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c REval.c -o REval.o
REval.c: In function ‘sjava_tryEval’:
REval.c:55:9: warning: passing argument 2 of ‘Rf_eval’ from incompatible pointer type [enabled by default]
/home/biocbuild/bbs-2.13-bioc/R/include/Rinternals.h:671:6: note: expected ‘SEXP’ but argument is of type ‘const struct JNINativeInterface_ **’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RFunctionListener.c -o RFunctionListener.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RReferenceCall.c -o RReferenceCall.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RStoJava.c -o RStoJava.o
RStoJava.c: In function ‘s_register_VM’:
RStoJava.c:360:17: warning: variable ‘msg’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RtoJava.c -o RtoJava.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RSJava/CtoJava.c -o RSJava/CtoJava.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RSJava/ErrorHandling.c -o RSJava/ErrorHandling.o
RSJava/ErrorHandling.c: In function ‘throw_Java_exception’:
RSJava/ErrorHandling.c:51:2: warning: implicit declaration of function ‘REprintf’ [-Wimplicit-function-declaration]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RSJava/ManagerInterfaceUtils.c -o RSJava/ManagerInterfaceUtils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RSJava/References.c -o RSJava/References.o
RSJava/References.c: In function ‘initReferenceClasses’:
RSJava/References.c:100:6: warning: implicit declaration of function ‘REprintf’ [-Wimplicit-function-declaration]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.13-bioc/R/include -I/home/biocbuild/bbs-2.13-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include -I/usr/lib/jvm/java-6-openjdk-amd64/jre/include/ -I/usr/local/include -fpic -g -O2 -Wall -c RSJava/JNIUtils.c -o RSJava/JNIUtils.o
RSJava/JNIUtils.c: In function ‘get_java_class_name’:
RSJava/JNIUtils.c:78:6: warning: implicit declaration of function ‘REprintf’ [-Wimplicit-function-declaration]
installing to /home/biocbuild/bbs-2.13-bioc/meat/SJava.Rcheck/SJava/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘merge’ from package ‘base’ in package ‘SJava’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (SJava)