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BioC 2.14: INSTALL report for SJava on zin2

This page was generated on 2014-10-08 08:48:37 -0700 (Wed, 08 Oct 2014).

Package 730/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SJava 0.90.0
Martin Morgan
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/SJava
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64 [ OK ] OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
petty Mac OS X Snow Leopard (10.6.8) / x86_64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
morelia Mac OS X Mavericks (10.9.5) / x86_64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...

Summary

Package: SJava
Version: 0.90.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD INSTALL SJava
StartedAt: 2014-10-07 18:06:36 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 18:06:47 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 10.3 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD INSTALL SJava
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-2.14-bioc/R/library’
* 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-2.14-bioc/meat/SJava/inst:/home/biocbuild/bbs-2.14-bioc/meat/SJava/inst/org/omegahat/Jars/Environment.jar -o RForeignReference.h org.omegahat.R.Java.RForeignReference
/usr/bin/javah -classpath /home/biocbuild/bbs-2.14-bioc/meat/SJava/inst:/home/biocbuild/bbs-2.14-bioc/meat/SJava/inst/org/omegahat/Jars/Environment.jar -o RManualFunctionActionListener.h org.omegahat.R.Java.RManualFunctionActionListener
/usr/bin/javah -classpath /home/biocbuild/bbs-2.14-bioc/meat/SJava/inst:/home/biocbuild/bbs-2.14-bioc/meat/SJava/inst/org/omegahat/Jars/Environment.jar -o ROmegahatInterpreter.h org.omegahat.R.Java.ROmegahatInterpreter
/usr/bin/javah -classpath /home/biocbuild/bbs-2.14-bioc/meat/SJava/inst:/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/meat/SJava/src/RSJava'
/usr/bin/javah -classpath /home/biocbuild/bbs-2.14-bioc/meat/SJava/inst:/home/biocbuild/bbs-2.14-bioc/meat/SJava/inst/org/omegahat/Jars/Environment.jar -o OmegaInterfaceManager.h \
	  org.omegahat.Interfaces.NativeInterface.OmegaInterfaceManager
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/meat/SJava/inst/include
make[1]: Leaving directory `/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include/Rinternals.h:756:6: note: expected ‘SEXP’ but argument is of type ‘const struct JNINativeInterface_ **’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-2.14-bioc/R/include -I/home/biocbuild/bbs-2.14-bioc/R/include/R_ext -I/home/biocbuild/bbs-2.14-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-2.14-bioc/meat/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-2.14-bioc/R/lib -lR
mkdir -p /home/biocbuild/bbs-2.14-bioc/R/library/SJava/libs
ln -s SJava.so /home/biocbuild/bbs-2.14-bioc/R/library/SJava/libs/libSJava.so
ln -s SJava.so /home/biocbuild/bbs-2.14-bioc/R/library/SJava/libs/libRInterpreter.so
installing to /home/biocbuild/bbs-2.14-bioc/R/library/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)