SJava 0.84.0
Martin Morgan
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/SJava | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / 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 Leopard (10.5.8) / i386 | N O T S U P P O R T E D |
* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘0.84.0’
* 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 whether package ‘SJava’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated 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
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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
JavaConstructor 0.488 0.328 10.945
JClass 0.536 0.184 8.613
* checking PDF version of manual ... OK
NOTE: There was 1 note.
See
‘/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00check.log’
for details.
* installing *source* package ‘SJava’ ...
configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
checking shlib support in R... checking Java support in R... present:
interpreter : '/usr/lib64/jvm/java/jre/bin/java'
archiver : '/usr/lib64/jvm/java/bin/jar'
compiler : '/usr/lib64/jvm/java/bin/javac'
header prep.: '/usr/lib64/jvm/java/bin/javah'
cpp flags : '-I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux'
java libs : '-L/usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/amd64/server -L/usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/amd64 -L/usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/../lib/amd64 -L/usr/local/lib64 -L/usr/lib64/mpi/gcc/openmpi/lib64 -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm'
Looking in /usr/lib64/jvm/java/include
Looking in /usr/lib64/jvm/java/include/linux
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/lib64/jvm/java/bin/javah -classpath /loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/Environment.jar -o RForeignReference.h org.omegahat.R.Java.RForeignReference
/usr/lib64/jvm/java/bin/javah -classpath /loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/Environment.jar -o RManualFunctionActionListener.h org.omegahat.R.Java.RManualFunctionActionListener
/usr/lib64/jvm/java/bin/javah -classpath /loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/Environment.jar -o ROmegahatInterpreter.h org.omegahat.R.Java.ROmegahatInterpreter
/usr/lib64/jvm/java/bin/javah -classpath /loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/loc/home/biocbuild/bbs-2.11-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 `/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava'
/usr/lib64/jvm/java/bin/javah -classpath /loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/loc/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -fpic -g -O2 -Wall -c CtoJava.c -o CtoJava.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -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-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -fpic -g -O2 -Wall -c ManagerInterfaceUtils.c -o ManagerInterfaceUtils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -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-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -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 /loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include
make[1]: Leaving directory `/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -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-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c Converters.c -o Converters.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c Reflectance.c -o Reflectance.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c REmbed.c -o REmbed.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c REmbedWin.c -o REmbedWin.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c REval.c -o REval.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c RFunctionListener.c -o RFunctionListener.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c RReferenceCall.c -o RReferenceCall.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -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-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c RtoJava.c -o RtoJava.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c RSJava/CtoJava.c -o RSJava/CtoJava.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -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-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c RSJava/ManagerInterfaceUtils.c -o RSJava/ManagerInterfaceUtils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -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-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -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/lib64 -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/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/amd64/server -L/usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/amd64 -L/usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/../lib/amd64 -L/usr/local/lib64 -L/usr/lib64/mpi/gcc/openmpi/lib64 -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
mkdir -p /loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/SJava/libs
ln -s SJava.so /loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/SJava/libs/libSJava.so
ln -s SJava.so /loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/SJava/libs/libRInterpreter.so
make -C RSJava
make[1]: Entering directory `/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -fpic -g -O2 -Wall -c CtoJava.c -o CtoJava.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -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-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -fpic -g -O2 -Wall -c ManagerInterfaceUtils.c -o ManagerInterfaceUtils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -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-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -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 /loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include
make[1]: Leaving directory `/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -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-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c Converters.c -o Converters.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c Reflectance.c -o Reflectance.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c REmbed.c -o REmbed.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c REmbedWin.c -o REmbedWin.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c REval.c -o REval.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c RFunctionListener.c -o RFunctionListener.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c RReferenceCall.c -o RReferenceCall.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -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-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c RtoJava.c -o RtoJava.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c RSJava/CtoJava.c -o RSJava/CtoJava.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -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-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c RSJava/ManagerInterfaceUtils.c -o RSJava/ManagerInterfaceUtils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -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-2.11-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.11-bioc/R/include -I/home/biocbuild/bbs-2.11-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava -I. -I/loc/home/biocbuild/bbs-2.11-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -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 /loc/home/biocbuild/bbs-2.11-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)