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BioC 3.4: CHECK report for SJava on zin1

This page was generated on 2016-05-02 10:49:05 -0700 (Mon, 02 May 2016).

Package 1084/1213HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SJava 0.97.2
Martin Morgan
Snapshot Date: 2016-05-01 16:20:05 -0700 (Sun, 01 May 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SJava
Last Changed Rev: 113181 / Revision: 116959
Last Changed Date: 2016-02-02 08:41:08 -0800 (Tue, 02 Feb 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  ERROR  OK [ ERROR ]
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...

Summary

Package: SJava
Version: 0.97.2
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SJava_0.97.2.tar.gz
StartedAt: 2016-05-01 23:36:17 -0700 (Sun, 01 May 2016)
EndedAt: 2016-05-01 23:36:30 -0700 (Sun, 01 May 2016)
EllapsedTime: 13.0 seconds
RetCode: 1
Status:  ERROR 
CheckDir: SJava.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SJava_0.97.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck’
* using R version 3.3.0 RC (2016-04-28 r70561)
* 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 ‘0.97.2’
* 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 ... [9s/9s] ERROR
Installation failed.
See ‘/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00install.out’ for details.
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-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-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/antlr.jar:/home/biocbuild/bbs-3.4-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-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/antlr.jar:/home/biocbuild/bbs-3.4-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-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/antlr.jar:/home/biocbuild/bbs-3.4-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-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/antlr.jar:/home/biocbuild/bbs-3.4-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-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava'
/usr/bin/javah -classpath /home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/org/omegahat/Jars/antlr.jar:/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-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-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava'
gcc -std=gnu99 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG -D_R_ -I/home/biocbuild/bbs-3.4-bioc/R/include -I/home/biocbuild/bbs-3.4-bioc/R/include/R_ext -I/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/home/biocbuild/bbs-3.4-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-3.4-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-3.4-bioc/R/lib -lR
/usr/bin/ld: cannot find -ljvm
collect2: error: ld returned 1 exit status
/home/biocbuild/bbs-3.4-bioc/R/share/make/shlib.mk:6: recipe for target 'SJava.so' failed
make: *** [SJava.so] Error 1
ERROR: compilation failed for package ‘SJava’
* removing ‘/home/biocbuild/bbs-3.4-bioc/meat/SJava.Rcheck/SJava’