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BioC 3.0: INSTALL report for SJava on zin1

This page was generated on 2015-04-10 09:38:32 -0700 (Fri, 10 Apr 2015).

Package 830/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SJava 0.92.1
Martin Morgan
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/SJava
Last Changed Rev: 99546 / Revision: 102249
Last Changed Date: 2015-02-17 10:57:35 -0800 (Tue, 17 Feb 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64 [ OK ] OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
perceval Mac OS X Snow Leopard (10.6.8) / x86_64 ...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: 0.92.1
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD INSTALL SJava
StartedAt: 2015-04-09 17:08:01 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 17:08:11 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 10.4 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD INSTALL SJava
###
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* installing to library ‘/home/biocbuild/bbs-3.0-bioc/R/library’
* 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-6-openjdk-amd64/jre/../include'
java libs   : '-L/usr/lib/jvm/java-6-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-3.0-bioc/meat/SJava/inst:/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/org/omegahat/Jars/antlr.jar:/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/org/omegahat/Jars/Environment.jar -o RForeignReference.h org.omegahat.R.Java.RForeignReference
/usr/bin/javah -classpath /home/biocbuild/bbs-3.0-bioc/meat/SJava/inst:/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/org/omegahat/Jars/antlr.jar:/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/org/omegahat/Jars/Environment.jar -o RManualFunctionActionListener.h org.omegahat.R.Java.RManualFunctionActionListener
/usr/bin/javah -classpath /home/biocbuild/bbs-3.0-bioc/meat/SJava/inst:/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/org/omegahat/Jars/antlr.jar:/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/org/omegahat/Jars/Environment.jar -o ROmegahatInterpreter.h org.omegahat.R.Java.ROmegahatInterpreter
/usr/bin/javah -classpath /home/biocbuild/bbs-3.0-bioc/meat/SJava/inst:/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/org/omegahat/Jars/antlr.jar:/home/biocbuild/bbs-3.0-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-3.0-bioc/meat/SJava/src/RSJava'
/usr/bin/javah -classpath /home/biocbuild/bbs-3.0-bioc/meat/SJava/inst:/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/org/omegahat/Jars/antlr.jar:/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/org/omegahat/Jars/Environment.jar -o OmegaInterfaceManager.h \
	  org.omegahat.Interfaces.NativeInterface.OmegaInterfaceManager
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/include  -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include  -fpic  -g -O2  -Wall -c ErrorHandling.c -o ErrorHandling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/include  -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include  -fpic  -g -O2  -Wall -c References.c -o References.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/include  -I/usr/lib/jvm/java-6-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-3.0-bioc/meat/SJava/inst/include
rm -f CtoJava.o ErrorHandling.o ManagerInterfaceUtils.o References.o JNIUtils.o
make[1]: Leaving directory `/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava'
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/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-3.0-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/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-3.0-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/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-3.0-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/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-3.0-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/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
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/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-3.0-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/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-3.0-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/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-3.0-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/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-3.0-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/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-3.0-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/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
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/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-3.0-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/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
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.0-bioc/R/include -I/home/biocbuild/bbs-3.0-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.0-bioc/meat/SJava/inst/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
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-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-6-openjdk-amd64/jre/lib/amd64/server -ljvm -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
mkdir -p /home/biocbuild/bbs-3.0-bioc/R/library/SJava/libs
ln -s SJava.so /home/biocbuild/bbs-3.0-bioc/R/library/SJava/libs/libSJava.so
ln -s SJava.so /home/biocbuild/bbs-3.0-bioc/R/library/SJava/libs/libRInterpreter.so
installing to /home/biocbuild/bbs-3.0-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)