BioC 2.9: CHECK report for SJava on wilson2

Package: SJava

Version: 0.79.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings SJava_0.79.0.tar.gz

StartedAt: 2011-05-09 14:17:35 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:18:06 -0700 (Mon, 09 May 2011)

EllapsedTime: 31.2 seconds

RetCode: 0

Status: OK

CheckDir: SJava.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘0.79.0’
* checking package dependencies ... OK
* checking if this is a source package ... 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 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 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 ... 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

* installing *source* package ‘SJava’ ...
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-sun-1.6.0/jre/lib/amd64/server -L/usr/lib64/jvm/java-1.6.0-sun-1.6.0/jre/lib/amd64 -L/usr/lib64/jvm/java-1.6.0-sun-1.6.0/jre/../lib/amd64 -L/usr/local/lib64 -L/usr/local/lib/root -L -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-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava'
/usr/lib64/jvm/java/bin/javah -classpath /loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst:/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include   -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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
cp CtoJava.h ErrorHandling.h ManagerInterfaceUtils.h References.h JNIUtils.h /loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/inst/include
make[1]: Leaving directory `/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -D_R_ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/home/biocbuild/bbs-2.9-bioc/R/include/R_ext -I/loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/00_pkg_src/SJava/src/RSJava  -I. -I/loc/home/biocbuild/bbs-2.9-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
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-sun-1.6.0/jre/lib/amd64/server -L/usr/lib64/jvm/java-1.6.0-sun-1.6.0/jre/lib/amd64 -L/usr/lib64/jvm/java-1.6.0-sun-1.6.0/jre/../lib/amd64 -L/usr/local/lib64 -L/usr/local/lib/root -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
mkdir -p /loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/SJava/libs
ln -s SJava.so /loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/SJava/libs/libSJava.so
ln -s SJava.so /loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/SJava/libs/libRInterpreter.so
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/SJava.Rcheck/SJava/libs
** R
** inst
** preparing package for lazy loading
Creating a new generic function for "merge" in "SJava"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (SJava)

name	user	system	elapsed
Array	0.132	0.020	0.151
Dollar	0.384	0.012	0.412
JClass	0.180	0.028	0.737
Java	0.028	0.000	0.028
JavaConfiguration-class	0.004	0.000	0.005
JavaConstructor	0.132	0.008	0.363
JavaInit	0	0	0
JavaTerminate	0	0	0
OmegahatExpression	0.004	0.000	0.001
RSJava.symbol	0	0	0
RtoJavaSig	0	0	0
expandClassName	0.020	0.000	0.013
foreignReference	0.024	0.000	0.024
getForeignReferences	0.292	0.032	0.312
getJavaConverterDescriptions	0	0	0
getJavaHandler	0.008	0.000	0.008
getMethods	0.076	0.000	0.078
getNumJavaConverters	0.000	0.000	0.001
interfaceGenerator	0.004	0.000	0.005
isJavaInitialized	0.044	0.000	0.076
javaConfig	0.004	0.000	0.006
javaHandlerGenerator	0	0	0
javaIs	0.000	0.000	0.002
jdynamicCompile	0.000	0.004	0.000
mergePath	0.000	0.000	0.001
mergeProperties	0.000	0.000	0.002
omegahatReference	0	0	0
removeJavaConverter	0	0	0
setJavaConverter	0	0	0
setJavaFunctionConverter	0.048	0.000	0.047
setJavaHandler	0	0	0

Summary

Command output