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BioC 3.3: CHECK report for SJava on zin2

This page was generated on 2016-10-13 12:42:08 -0700 (Thu, 13 Oct 2016).

Package 1082/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SJava 0.98.0
Martin Morgan
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/SJava
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
oaxaca Mac OS X Mavericks (10.9.5) / x86_64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...

Summary

Package: SJava
Version: 0.98.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SJava_0.98.0.tar.gz
StartedAt: 2016-10-13 06:54:50 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 06:55:20 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 29.9 seconds
RetCode: 0
Status:  OK 
CheckDir: SJava.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SJava_0.98.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SJava/DESCRIPTION’ ... OK
* this is package ‘SJava’ version ‘0.98.0’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... 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 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 ... OK
* 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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘SJava/libs/SJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_Interactive’,
    ‘Rf_endEmbeddedR’, ‘Rf_initialize_R’, ‘run_Rmainloop’,
    ‘setup_Rmainloop’
File ‘SJava/libs/libRInterpreter.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_Interactive’,
    ‘Rf_endEmbeddedR’, ‘Rf_initialize_R’, ‘run_Rmainloop’,
    ‘setup_Rmainloop’
File ‘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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00check.log’
for details.

SJava.Rcheck/00install.out:

* installing *source* package ‘SJava’ ...
checking shlib support in R... yes
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-7-openjdk-amd64/jre/../include'
java libs   : '-L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm'
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
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-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/antlr.jar:/home/biocbuild/bbs-3.3-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-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/antlr.jar:/home/biocbuild/bbs-3.3-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-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/antlr.jar:/home/biocbuild/bbs-3.3-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-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/antlr.jar:/home/biocbuild/bbs-3.3-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-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava'
/usr/bin/javah -classpath /home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/antlr.jar:/home/biocbuild/bbs-3.3-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-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include  -fpic  -g -O2  -Wall -c CtoJava.c -o CtoJava.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include  -fpic  -g -O2  -Wall -c ErrorHandling.c -o ErrorHandling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include  -fpic  -g -O2  -Wall -c ManagerInterfaceUtils.c -o ManagerInterfaceUtils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include  -fpic  -g -O2  -Wall -c References.c -o References.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include  -fpic  -g -O2  -Wall -c JNIUtils.c -o JNIUtils.o
cp CtoJava.h ErrorHandling.h ManagerInterfaceUtils.h References.h JNIUtils.h /home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include
rm -f CtoJava.o ErrorHandling.o ManagerInterfaceUtils.o References.o JNIUtils.o
make[1]: Leaving directory `/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava'
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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]
     USER_OBJECT_ fun;
                  ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include -I/usr/local/include    -fpic  -g -O2  -Wall -c REval.c -o REval.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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]
     const char *msg;
                 ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include -I/usr/local/include    -fpic  -g -O2  -Wall -c RSJava/ErrorHandling.c -o RSJava/ErrorHandling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include -I/usr/local/include    -fpic  -g -O2  -Wall -c RSJava/References.c -o RSJava/References.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include -I/usr/local/include    -fpic  -g -O2  -Wall -c RSJava/JNIUtils.c -o RSJava/JNIUtils.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o SJava.so ConverterExamples.o Converters.o Reflectance.o REmbed.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-7-openjdk-amd64/jre/lib/amd64/server -ljvm -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
mkdir -p /home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/SJava/libs
ln -s SJava.so /home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/SJava/libs/libSJava.so
ln -s SJava.so /home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/SJava/libs/libRInterpreter.so
make -C RSJava
make[1]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava'
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include  -fpic  -g -O2  -Wall -c CtoJava.c -o CtoJava.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include  -fpic  -g -O2  -Wall -c ErrorHandling.c -o ErrorHandling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include  -fpic  -g -O2  -Wall -c ManagerInterfaceUtils.c -o ManagerInterfaceUtils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include  -fpic  -g -O2  -Wall -c References.c -o References.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include  -fpic  -g -O2  -Wall -c JNIUtils.c -o JNIUtils.o
cp CtoJava.h ErrorHandling.h ManagerInterfaceUtils.h References.h JNIUtils.h /home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include
rm -f CtoJava.o ErrorHandling.o ManagerInterfaceUtils.o References.o JNIUtils.o
make[1]: Leaving directory `/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava'
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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]
     USER_OBJECT_ fun;
                  ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include -I/usr/local/include    -fpic  -g -O2  -Wall -c REval.c -o REval.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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]
     const char *msg;
                 ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include -I/usr/local/include    -fpic  -g -O2  -Wall -c RSJava/ErrorHandling.c -o RSJava/ErrorHandling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-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-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include -I/usr/local/include    -fpic  -g -O2  -Wall -c RSJava/References.c -o RSJava/References.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.3-bioc/R/include -I/home/biocbuild/bbs-3.3-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.3-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include  -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include -I/usr/local/include    -fpic  -g -O2  -Wall -c RSJava/JNIUtils.c -o RSJava/JNIUtils.o
installing to /home/biocbuild/bbs-3.3-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)

SJava.Rcheck/SJava-Ex.timings:

nameusersystemelapsed
Array0.1770.0080.183
Dollar0.6160.0080.635
JClass0.1810.0140.477
Java0.0290.0000.029
JavaConfiguration-class0.0030.0000.004
JavaConstructor0.1790.0080.302
JavaInit0.0010.0000.000
JavaTerminate0.0010.0000.001
OmegahatExpression0.0010.0040.002
RSJava.symbol0.0010.0000.001
RtoJavaSig0.0020.0000.000
expandClassName0.0320.0000.016
foreignReference0.0420.0080.026
getForeignReferences0.3890.0240.388
getJavaConverterDescriptions0.0010.0000.001
getJavaHandler0.0020.0040.005
getMethods0.0890.0040.094
getNumJavaConverters0.0010.0000.001
interfaceGenerator0.0060.0000.005
isJavaInitialized0.0520.0040.042
javaConfig0.0040.0000.003
javaHandlerGenerator0.0010.0000.000
javaIs0.0030.0000.003
jdynamicCompile0.0010.0000.001
mergePath0.0010.0000.001
mergeProperties0.0020.0000.002
omegahatReference0.0000.0000.001
removeJavaConverter0.0020.0000.001
setJavaConverter000
setJavaFunctionConverter0.0710.0000.071
setJavaHandler000