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Package 316/354HostnameOS / ArchBUILDCHECKBUILD BIN
SJava 0.73.0
Martin Morgan
Bioconductor Changelog
Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SJava
Last Changed Rev: 42686 / Revision: 43434
Last Changed Date: 2009-10-27 16:45:24 -0700 (Tue, 27 Oct 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ ERROR ] OK 
pitt Mac OS X Tiger (10.4.11) / i386 N O T   S U P P O R T E D
pelham Mac OS X Leopard (10.5.8) / i386 N O T   S U P P O R T E D
Package: SJava
Version: 0.73.0
Command: E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes SJava_0.73.0.tar.gz
StartedAt: 2009-12-07 18:31:51 -0800 (Mon, 07 Dec 2009)
EndedAt: 2009-12-07 18:32:13 -0800 (Mon, 07 Dec 2009)
EllapsedTime: 21.8 seconds
RetCode: 1
Status: ERROR
CheckDir: SJava.Rcheck
Warnings: NA

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/SJava.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-10-22 r50179)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SJava/DESCRIPTION' ... OK
* this is package 'SJava' version '0.73.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'SJava' can be installed ... WARNING
Found the following significant warnings:
  Converters.c:123: warning: 'index' is used uninitialized in this function
See 'E:/biocbld/bbs-2.6-bioc/meat/SJava.Rcheck/00install.out' for details.
* checking package directory ... OK
* checking for portable file names ... 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 ... ERROR
Error in inDL(x, as.logical(local), as.logical(now), ...) : 
  unable to load shared library 'E:/biocbld/bbs-2.6-bioc/meat/SJava.Rcheck/SJava/libs/SJava.dll':
  LoadLibrary failure:  The specified module could not be found.


Error in library(SJava) : .First.lib failed for 'SJava'
Execution halted

It looks like this package has a loading problem: see the messages for
details.

SJava.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'SJava' ...
** libs
  making DLL ...
C:/JDK/jdk1.6.0_16/bin/javah -classpath ../inst -o RForeignReference.h org.omegahat.R.Java.RForeignReference
C:/JDK/jdk1.6.0_16/bin/javah -classpath ../inst -o RSJava/OmegaInterfaceManager.h \
org.omegahat.Interfaces.NativeInterface.OmegaInterfaceManager
C:/JDK/jdk1.6.0_16/bin/javah -classpath ../inst -o RManualFunctionActionListener.h org.omegahat.R.Java.RManualFunctionActionListener
C:/JDK/jdk1.6.0_16/bin/javah -classpath ../inst -o RSJava/OmegaInterfaceManager.h \
org.omegahat.Interfaces.NativeInterface.OmegaInterfaceManager
C:/JDK/jdk1.6.0_16/bin/javah -classpath ../inst -o ROmegahatInterpreter.h org.omegahat.R.Java.ROmegahatInterpreter
C:/JDK/jdk1.6.0_16/bin/javah -classpath ../inst -o RSJava/OmegaInterfaceManager.h \
org.omegahat.Interfaces.NativeInterface.OmegaInterfaceManager
C:/JDK/jdk1.6.0_16/bin/javah -classpath ../inst -o REvaluator.h org.omegahat.R.Java.REvaluator
C:/JDK/jdk1.6.0_16/bin/javah -classpath ../inst -o RSJava/OmegaInterfaceManager.h \
org.omegahat.Interfaces.NativeInterface.OmegaInterfaceManager
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -D_R_ -DWin32 -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava    -v   -O3 -Wall  -std=gnu99 -c ConverterExamples.c -o ConverterExamples.o
Using built-in specs.
Target: mingw32
Configured with: ../gcc-4.2.1-2-src/configure --with-gcc --enable-libgomp --host=mingw32 --build=mingw32 --target=mingw32 --program-suffix=-sjlj --with-arch=i486 --with-tune=generic --disable-werror --prefix=/mingw --with-local-prefix=/mingw --enable-threads --disable-nls --enable-languages=c,c++,fortran,objc,obj-c++,ada --disable-win32-registry --enable-sjlj-exceptions --enable-libstdcxx-debug --enable-cxx-flags=-fno-function-sections -fno-data-sections --enable-version-specific-runtime-libs --disable-bootstrap
Thread model: win32
gcc version 4.2.1-sjlj (mingw32-2)
 c:/rtools/mingw/bin/../libexec/gcc/mingw32/4.2.1-sjlj/cc1.exe -quiet -v -Ie:/biocbld/bbs-2.6-bioc/R/include -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava -iprefix c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/ -D_R_ -DWin32 ConverterExamples.c -quiet -dumpbase ConverterExamples.c -mtune=generic -march=i486 -auxbase-strip ConverterExamples.o -O3 -Wall -std=gnu99 -version -o e:\biocbld\bbs-2.6-bioc\tmpdir/ccsAET7u.s
ignoring nonexistent directory "c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/include"
ignoring nonexistent directory "/mingw/include"
ignoring nonexistent directory "/mingw/lib/gcc/mingw32/4.2.1-sjlj/include"
ignoring nonexistent directory "/mingw/mingw32/include"
ignoring nonexistent directory "/mingw/include"
#include "..." search starts here:
#include <...> search starts here:
 e:/biocbld/bbs-2.6-bioc/R/include
 C:/JDK/jdk1.6.0_16/include
 C:/JDK/jdk1.6.0_16/include/win32
 e:/biocbld/bbs-2.6-bioc/R/include
 e:/biocbld/bbs-2.6-bioc/R/include/R_ext
 ../inst/include
 ../src/RSJava
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/include
End of search list.
GNU C version 4.2.1-sjlj (mingw32-2) (mingw32)
	compiled by GNU C version 4.2.1 (mingw32-dw2-1).
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 5a206dd7daa613ab6fd5107577c565b8
 c:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/bin/as.exe -o ConverterExamples.o e:\biocbld\bbs-2.6-bioc\tmpdir/ccsAET7u.s
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -D_R_ -DWin32 -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava    -v   -O3 -Wall  -std=gnu99 -c Converters.c -o Converters.o
Using built-in specs.
Target: mingw32
Configured with: ../gcc-4.2.1-2-src/configure --with-gcc --enable-libgomp --host=mingw32 --build=mingw32 --target=mingw32 --program-suffix=-sjlj --with-arch=i486 --with-tune=generic --disable-werror --prefix=/mingw --with-local-prefix=/mingw --enable-threads --disable-nls --enable-languages=c,c++,fortran,objc,obj-c++,ada --disable-win32-registry --enable-sjlj-exceptions --enable-libstdcxx-debug --enable-cxx-flags=-fno-function-sections -fno-data-sections --enable-version-specific-runtime-libs --disable-bootstrap
Thread model: win32
gcc version 4.2.1-sjlj (mingw32-2)
 c:/rtools/mingw/bin/../libexec/gcc/mingw32/4.2.1-sjlj/cc1.exe -quiet -v -Ie:/biocbld/bbs-2.6-bioc/R/include -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava -iprefix c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/ -D_R_ -DWin32 Converters.c -quiet -dumpbase Converters.c -mtune=generic -march=i486 -auxbase-strip Converters.o -O3 -Wall -std=gnu99 -version -o e:\biocbld\bbs-2.6-bioc\tmpdir/ccomLl4P.s
ignoring nonexistent directory "c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/include"
ignoring nonexistent directory "/mingw/include"
ignoring nonexistent directory "/mingw/lib/gcc/mingw32/4.2.1-sjlj/include"
ignoring nonexistent directory "/mingw/mingw32/include"
ignoring nonexistent directory "/mingw/include"
#include "..." search starts here:
#include <...> search starts here:
 e:/biocbld/bbs-2.6-bioc/R/include
 C:/JDK/jdk1.6.0_16/include
 C:/JDK/jdk1.6.0_16/include/win32
 e:/biocbld/bbs-2.6-bioc/R/include
 e:/biocbld/bbs-2.6-bioc/R/include/R_ext
 ../inst/include
 ../src/RSJava
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/include
End of search list.
GNU C version 4.2.1-sjlj (mingw32-2) (mingw32)
	compiled by GNU C version 4.2.1 (mingw32-dw2-1).
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 5a206dd7daa613ab6fd5107577c565b8
Converters.c: In function 'RS_JAVA_registerConverter':
Converters.c:123: warning: 'index' is used uninitialized in this function
Converters.c:631: note: 'index' was declared here
 c:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/bin/as.exe -o Converters.o e:\biocbld\bbs-2.6-bioc\tmpdir/ccomLl4P.s
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -D_R_ -DWin32 -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava    -v   -O3 -Wall  -std=gnu99 -c Reflectance.c -o Reflectance.o
Using built-in specs.
Target: mingw32
Configured with: ../gcc-4.2.1-2-src/configure --with-gcc --enable-libgomp --host=mingw32 --build=mingw32 --target=mingw32 --program-suffix=-sjlj --with-arch=i486 --with-tune=generic --disable-werror --prefix=/mingw --with-local-prefix=/mingw --enable-threads --disable-nls --enable-languages=c,c++,fortran,objc,obj-c++,ada --disable-win32-registry --enable-sjlj-exceptions --enable-libstdcxx-debug --enable-cxx-flags=-fno-function-sections -fno-data-sections --enable-version-specific-runtime-libs --disable-bootstrap
Thread model: win32
gcc version 4.2.1-sjlj (mingw32-2)
 c:/rtools/mingw/bin/../libexec/gcc/mingw32/4.2.1-sjlj/cc1.exe -quiet -v -Ie:/biocbld/bbs-2.6-bioc/R/include -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava -iprefix c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/ -D_R_ -DWin32 Reflectance.c -quiet -dumpbase Reflectance.c -mtune=generic -march=i486 -auxbase-strip Reflectance.o -O3 -Wall -std=gnu99 -version -o e:\biocbld\bbs-2.6-bioc\tmpdir/ccF4v19b.s
ignoring nonexistent directory "c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/include"
ignoring nonexistent directory "/mingw/include"
ignoring nonexistent directory "/mingw/lib/gcc/mingw32/4.2.1-sjlj/include"
ignoring nonexistent directory "/mingw/mingw32/include"
ignoring nonexistent directory "/mingw/include"
#include "..." search starts here:
#include <...> search starts here:
 e:/biocbld/bbs-2.6-bioc/R/include
 C:/JDK/jdk1.6.0_16/include
 C:/JDK/jdk1.6.0_16/include/win32
 e:/biocbld/bbs-2.6-bioc/R/include
 e:/biocbld/bbs-2.6-bioc/R/include/R_ext
 ../inst/include
 ../src/RSJava
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/include
End of search list.
GNU C version 4.2.1-sjlj (mingw32-2) (mingw32)
	compiled by GNU C version 4.2.1 (mingw32-dw2-1).
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 5a206dd7daa613ab6fd5107577c565b8
 c:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/bin/as.exe -o Reflectance.o e:\biocbld\bbs-2.6-bioc\tmpdir/ccF4v19b.s
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -D_R_ -DWin32 -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava    -v   -O3 -Wall  -std=gnu99 -c REmbed.c -o REmbed.o
Using built-in specs.
Target: mingw32
Configured with: ../gcc-4.2.1-2-src/configure --with-gcc --enable-libgomp --host=mingw32 --build=mingw32 --target=mingw32 --program-suffix=-sjlj --with-arch=i486 --with-tune=generic --disable-werror --prefix=/mingw --with-local-prefix=/mingw --enable-threads --disable-nls --enable-languages=c,c++,fortran,objc,obj-c++,ada --disable-win32-registry --enable-sjlj-exceptions --enable-libstdcxx-debug --enable-cxx-flags=-fno-function-sections -fno-data-sections --enable-version-specific-runtime-libs --disable-bootstrap
Thread model: win32
gcc version 4.2.1-sjlj (mingw32-2)
 c:/rtools/mingw/bin/../libexec/gcc/mingw32/4.2.1-sjlj/cc1.exe -quiet -v -Ie:/biocbld/bbs-2.6-bioc/R/include -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava -iprefix c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/ -D_R_ -DWin32 REmbed.c -quiet -dumpbase REmbed.c -mtune=generic -march=i486 -auxbase-strip REmbed.o -O3 -Wall -std=gnu99 -version -o e:\biocbld\bbs-2.6-bioc\tmpdir/ccZMxlSv.s
ignoring nonexistent directory "c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/include"
ignoring nonexistent directory "/mingw/include"
ignoring nonexistent directory "/mingw/lib/gcc/mingw32/4.2.1-sjlj/include"
ignoring nonexistent directory "/mingw/mingw32/include"
ignoring nonexistent directory "/mingw/include"
#include "..." search starts here:
#include <...> search starts here:
 e:/biocbld/bbs-2.6-bioc/R/include
 C:/JDK/jdk1.6.0_16/include
 C:/JDK/jdk1.6.0_16/include/win32
 e:/biocbld/bbs-2.6-bioc/R/include
 e:/biocbld/bbs-2.6-bioc/R/include/R_ext
 ../inst/include
 ../src/RSJava
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/include
End of search list.
GNU C version 4.2.1-sjlj (mingw32-2) (mingw32)
	compiled by GNU C version 4.2.1 (mingw32-dw2-1).
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 5a206dd7daa613ab6fd5107577c565b8
 c:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/bin/as.exe -o REmbed.o e:\biocbld\bbs-2.6-bioc\tmpdir/ccZMxlSv.s
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -D_R_ -DWin32 -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava    -v   -O3 -Wall  -std=gnu99 -c REval.c -o REval.o
Using built-in specs.
Target: mingw32
Configured with: ../gcc-4.2.1-2-src/configure --with-gcc --enable-libgomp --host=mingw32 --build=mingw32 --target=mingw32 --program-suffix=-sjlj --with-arch=i486 --with-tune=generic --disable-werror --prefix=/mingw --with-local-prefix=/mingw --enable-threads --disable-nls --enable-languages=c,c++,fortran,objc,obj-c++,ada --disable-win32-registry --enable-sjlj-exceptions --enable-libstdcxx-debug --enable-cxx-flags=-fno-function-sections -fno-data-sections --enable-version-specific-runtime-libs --disable-bootstrap
Thread model: win32
gcc version 4.2.1-sjlj (mingw32-2)
 c:/rtools/mingw/bin/../libexec/gcc/mingw32/4.2.1-sjlj/cc1.exe -quiet -v -Ie:/biocbld/bbs-2.6-bioc/R/include -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava -iprefix c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/ -D_R_ -DWin32 REval.c -quiet -dumpbase REval.c -mtune=generic -march=i486 -auxbase-strip REval.o -O3 -Wall -std=gnu99 -version -o e:\biocbld\bbs-2.6-bioc\tmpdir/ccVSg1xJ.s
ignoring nonexistent directory "c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/include"
ignoring nonexistent directory "/mingw/include"
ignoring nonexistent directory "/mingw/lib/gcc/mingw32/4.2.1-sjlj/include"
ignoring nonexistent directory "/mingw/mingw32/include"
ignoring nonexistent directory "/mingw/include"
#include "..." search starts here:
#include <...> search starts here:
 e:/biocbld/bbs-2.6-bioc/R/include
 C:/JDK/jdk1.6.0_16/include
 C:/JDK/jdk1.6.0_16/include/win32
 e:/biocbld/bbs-2.6-bioc/R/include
 e:/biocbld/bbs-2.6-bioc/R/include/R_ext
 ../inst/include
 ../src/RSJava
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/include
End of search list.
GNU C version 4.2.1-sjlj (mingw32-2) (mingw32)
	compiled by GNU C version 4.2.1 (mingw32-dw2-1).
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 5a206dd7daa613ab6fd5107577c565b8
 c:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/bin/as.exe -o REval.o e:\biocbld\bbs-2.6-bioc\tmpdir/ccVSg1xJ.s
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -D_R_ -DWin32 -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava    -v   -O3 -Wall  -std=gnu99 -c RFunctionListener.c -o RFunctionListener.o
Using built-in specs.
Target: mingw32
Configured with: ../gcc-4.2.1-2-src/configure --with-gcc --enable-libgomp --host=mingw32 --build=mingw32 --target=mingw32 --program-suffix=-sjlj --with-arch=i486 --with-tune=generic --disable-werror --prefix=/mingw --with-local-prefix=/mingw --enable-threads --disable-nls --enable-languages=c,c++,fortran,objc,obj-c++,ada --disable-win32-registry --enable-sjlj-exceptions --enable-libstdcxx-debug --enable-cxx-flags=-fno-function-sections -fno-data-sections --enable-version-specific-runtime-libs --disable-bootstrap
Thread model: win32
gcc version 4.2.1-sjlj (mingw32-2)
 c:/rtools/mingw/bin/../libexec/gcc/mingw32/4.2.1-sjlj/cc1.exe -quiet -v -Ie:/biocbld/bbs-2.6-bioc/R/include -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava -iprefix c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/ -D_R_ -DWin32 RFunctionListener.c -quiet -dumpbase RFunctionListener.c -mtune=generic -march=i486 -auxbase-strip RFunctionListener.o -O3 -Wall -std=gnu99 -version -o e:\biocbld\bbs-2.6-bioc\tmpdir/ccf5yVj1.s
ignoring nonexistent directory "c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/include"
ignoring nonexistent directory "/mingw/include"
ignoring nonexistent directory "/mingw/lib/gcc/mingw32/4.2.1-sjlj/include"
ignoring nonexistent directory "/mingw/mingw32/include"
ignoring nonexistent directory "/mingw/include"
#include "..." search starts here:
#include <...> search starts here:
 e:/biocbld/bbs-2.6-bioc/R/include
 C:/JDK/jdk1.6.0_16/include
 C:/JDK/jdk1.6.0_16/include/win32
 e:/biocbld/bbs-2.6-bioc/R/include
 e:/biocbld/bbs-2.6-bioc/R/include/R_ext
 ../inst/include
 ../src/RSJava
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/include
End of search list.
GNU C version 4.2.1-sjlj (mingw32-2) (mingw32)
	compiled by GNU C version 4.2.1 (mingw32-dw2-1).
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 5a206dd7daa613ab6fd5107577c565b8
 c:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/bin/as.exe -o RFunctionListener.o e:\biocbld\bbs-2.6-bioc\tmpdir/ccf5yVj1.s
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -D_R_ -DWin32 -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava    -v   -O3 -Wall  -std=gnu99 -c RReferenceCall.c -o RReferenceCall.o
Using built-in specs.
Target: mingw32
Configured with: ../gcc-4.2.1-2-src/configure --with-gcc --enable-libgomp --host=mingw32 --build=mingw32 --target=mingw32 --program-suffix=-sjlj --with-arch=i486 --with-tune=generic --disable-werror --prefix=/mingw --with-local-prefix=/mingw --enable-threads --disable-nls --enable-languages=c,c++,fortran,objc,obj-c++,ada --disable-win32-registry --enable-sjlj-exceptions --enable-libstdcxx-debug --enable-cxx-flags=-fno-function-sections -fno-data-sections --enable-version-specific-runtime-libs --disable-bootstrap
Thread model: win32
gcc version 4.2.1-sjlj (mingw32-2)
 c:/rtools/mingw/bin/../libexec/gcc/mingw32/4.2.1-sjlj/cc1.exe -quiet -v -Ie:/biocbld/bbs-2.6-bioc/R/include -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava -iprefix c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/ -D_R_ -DWin32 RReferenceCall.c -quiet -dumpbase RReferenceCall.c -mtune=generic -march=i486 -auxbase-strip RReferenceCall.o -O3 -Wall -std=gnu99 -version -o e:\biocbld\bbs-2.6-bioc\tmpdir/cczBucCd.s
ignoring nonexistent directory "c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/include"
ignoring nonexistent directory "/mingw/include"
ignoring nonexistent directory "/mingw/lib/gcc/mingw32/4.2.1-sjlj/include"
ignoring nonexistent directory "/mingw/mingw32/include"
ignoring nonexistent directory "/mingw/include"
#include "..." search starts here:
#include <...> search starts here:
 e:/biocbld/bbs-2.6-bioc/R/include
 C:/JDK/jdk1.6.0_16/include
 C:/JDK/jdk1.6.0_16/include/win32
 e:/biocbld/bbs-2.6-bioc/R/include
 e:/biocbld/bbs-2.6-bioc/R/include/R_ext
 ../inst/include
 ../src/RSJava
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/include
End of search list.
GNU C version 4.2.1-sjlj (mingw32-2) (mingw32)
	compiled by GNU C version 4.2.1 (mingw32-dw2-1).
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 5a206dd7daa613ab6fd5107577c565b8
 c:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/bin/as.exe -o RReferenceCall.o e:\biocbld\bbs-2.6-bioc\tmpdir/cczBucCd.s
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -D_R_ -DWin32 -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava    -v   -O3 -Wall  -std=gnu99 -c RStoJava.c -o RStoJava.o
Using built-in specs.
Target: mingw32
Configured with: ../gcc-4.2.1-2-src/configure --with-gcc --enable-libgomp --host=mingw32 --build=mingw32 --target=mingw32 --program-suffix=-sjlj --with-arch=i486 --with-tune=generic --disable-werror --prefix=/mingw --with-local-prefix=/mingw --enable-threads --disable-nls --enable-languages=c,c++,fortran,objc,obj-c++,ada --disable-win32-registry --enable-sjlj-exceptions --enable-libstdcxx-debug --enable-cxx-flags=-fno-function-sections -fno-data-sections --enable-version-specific-runtime-libs --disable-bootstrap
Thread model: win32
gcc version 4.2.1-sjlj (mingw32-2)
 c:/rtools/mingw/bin/../libexec/gcc/mingw32/4.2.1-sjlj/cc1.exe -quiet -v -Ie:/biocbld/bbs-2.6-bioc/R/include -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava -iprefix c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/ -D_R_ -DWin32 RStoJava.c -quiet -dumpbase RStoJava.c -mtune=generic -march=i486 -auxbase-strip RStoJava.o -O3 -Wall -std=gnu99 -version -o e:\biocbld\bbs-2.6-bioc\tmpdir/cc2dr4Fh.s
ignoring nonexistent directory "c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/include"
ignoring nonexistent directory "/mingw/include"
ignoring nonexistent directory "/mingw/lib/gcc/mingw32/4.2.1-sjlj/include"
ignoring nonexistent directory "/mingw/mingw32/include"
ignoring nonexistent directory "/mingw/include"
#include "..." search starts here:
#include <...> search starts here:
 e:/biocbld/bbs-2.6-bioc/R/include
 C:/JDK/jdk1.6.0_16/include
 C:/JDK/jdk1.6.0_16/include/win32
 e:/biocbld/bbs-2.6-bioc/R/include
 e:/biocbld/bbs-2.6-bioc/R/include/R_ext
 ../inst/include
 ../src/RSJava
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/include
End of search list.
GNU C version 4.2.1-sjlj (mingw32-2) (mingw32)
	compiled by GNU C version 4.2.1 (mingw32-dw2-1).
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 5a206dd7daa613ab6fd5107577c565b8
RStoJava.c: In function 's_start_VM':
RStoJava.c:392: warning: format '%d' expects type 'int', but argument 3 has type 'jsize'
RStoJava.c: In function 'RS_genericJavaCall':
RStoJava.c:551: warning: format '%d' expects type 'int', but argument 4 has type 'jint'
 c:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/bin/as.exe -o RStoJava.o e:\biocbld\bbs-2.6-bioc\tmpdir/cc2dr4Fh.s
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -D_R_ -DWin32 -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava    -v   -O3 -Wall  -std=gnu99 -c RtoJava.c -o RtoJava.o
Using built-in specs.
Target: mingw32
Configured with: ../gcc-4.2.1-2-src/configure --with-gcc --enable-libgomp --host=mingw32 --build=mingw32 --target=mingw32 --program-suffix=-sjlj --with-arch=i486 --with-tune=generic --disable-werror --prefix=/mingw --with-local-prefix=/mingw --enable-threads --disable-nls --enable-languages=c,c++,fortran,objc,obj-c++,ada --disable-win32-registry --enable-sjlj-exceptions --enable-libstdcxx-debug --enable-cxx-flags=-fno-function-sections -fno-data-sections --enable-version-specific-runtime-libs --disable-bootstrap
Thread model: win32
gcc version 4.2.1-sjlj (mingw32-2)
 c:/rtools/mingw/bin/../libexec/gcc/mingw32/4.2.1-sjlj/cc1.exe -quiet -v -Ie:/biocbld/bbs-2.6-bioc/R/include -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava -iprefix c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/ -D_R_ -DWin32 RtoJava.c -quiet -dumpbase RtoJava.c -mtune=generic -march=i486 -auxbase-strip RtoJava.o -O3 -Wall -std=gnu99 -version -o e:\biocbld\bbs-2.6-bioc\tmpdir/cc273YQL.s
ignoring nonexistent directory "c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/include"
ignoring nonexistent directory "/mingw/include"
ignoring nonexistent directory "/mingw/lib/gcc/mingw32/4.2.1-sjlj/include"
ignoring nonexistent directory "/mingw/mingw32/include"
ignoring nonexistent directory "/mingw/include"
#include "..." search starts here:
#include <...> search starts here:
 e:/biocbld/bbs-2.6-bioc/R/include
 C:/JDK/jdk1.6.0_16/include
 C:/JDK/jdk1.6.0_16/include/win32
 e:/biocbld/bbs-2.6-bioc/R/include
 e:/biocbld/bbs-2.6-bioc/R/include/R_ext
 ../inst/include
 ../src/RSJava
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/include
End of search list.
GNU C version 4.2.1-sjlj (mingw32-2) (mingw32)
	compiled by GNU C version 4.2.1 (mingw32-dw2-1).
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 5a206dd7daa613ab6fd5107577c565b8
 c:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/bin/as.exe -o RtoJava.o e:\biocbld\bbs-2.6-bioc\tmpdir/cc273YQL.s
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -D_R_ -DWin32 -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava    -v   -O3 -Wall  -std=gnu99 -c RSJava/CtoJava.c -o RSJava/CtoJava.o
Using built-in specs.
Target: mingw32
Configured with: ../gcc-4.2.1-2-src/configure --with-gcc --enable-libgomp --host=mingw32 --build=mingw32 --target=mingw32 --program-suffix=-sjlj --with-arch=i486 --with-tune=generic --disable-werror --prefix=/mingw --with-local-prefix=/mingw --enable-threads --disable-nls --enable-languages=c,c++,fortran,objc,obj-c++,ada --disable-win32-registry --enable-sjlj-exceptions --enable-libstdcxx-debug --enable-cxx-flags=-fno-function-sections -fno-data-sections --enable-version-specific-runtime-libs --disable-bootstrap
Thread model: win32
gcc version 4.2.1-sjlj (mingw32-2)
 c:/rtools/mingw/bin/../libexec/gcc/mingw32/4.2.1-sjlj/cc1.exe -quiet -v -Ie:/biocbld/bbs-2.6-bioc/R/include -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava -iprefix c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/ -D_R_ -DWin32 RSJava/CtoJava.c -quiet -dumpbase CtoJava.c -mtune=generic -march=i486 -auxbase-strip RSJava/CtoJava.o -O3 -Wall -std=gnu99 -version -o e:\biocbld\bbs-2.6-bioc\tmpdir/ccsXAYE2.s
ignoring nonexistent directory "c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/include"
ignoring nonexistent directory "/mingw/include"
ignoring nonexistent directory "/mingw/lib/gcc/mingw32/4.2.1-sjlj/include"
ignoring nonexistent directory "/mingw/mingw32/include"
ignoring nonexistent directory "/mingw/include"
#include "..." search starts here:
#include <...> search starts here:
 e:/biocbld/bbs-2.6-bioc/R/include
 C:/JDK/jdk1.6.0_16/include
 C:/JDK/jdk1.6.0_16/include/win32
 e:/biocbld/bbs-2.6-bioc/R/include
 e:/biocbld/bbs-2.6-bioc/R/include/R_ext
 ../inst/include
 ../src/RSJava
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/include
End of search list.
GNU C version 4.2.1-sjlj (mingw32-2) (mingw32)
	compiled by GNU C version 4.2.1 (mingw32-dw2-1).
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 5a206dd7daa613ab6fd5107577c565b8
RSJava/CtoJava.c: In function 'getJNIEnv':
RSJava/CtoJava.c:1062: warning: dereferencing type-punned pointer will break strict-aliasing rules
RSJava/CtoJava.c: In function 'getThreadJNIEnv':
RSJava/CtoJava.c:1104: warning: dereferencing type-punned pointer will break strict-aliasing rules
RSJava/CtoJava.c:1108: warning: dereferencing type-punned pointer will break strict-aliasing rules
RSJava/CtoJava.c:1112: warning: dereferencing type-punned pointer will break strict-aliasing rules
 c:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/bin/as.exe -o RSJava/CtoJava.o e:\biocbld\bbs-2.6-bioc\tmpdir/ccsXAYE2.s
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -D_R_ -DWin32 -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava    -v   -O3 -Wall  -std=gnu99 -c RSJava/ErrorHandling.c -o RSJava/ErrorHandling.o
Using built-in specs.
Target: mingw32
Configured with: ../gcc-4.2.1-2-src/configure --with-gcc --enable-libgomp --host=mingw32 --build=mingw32 --target=mingw32 --program-suffix=-sjlj --with-arch=i486 --with-tune=generic --disable-werror --prefix=/mingw --with-local-prefix=/mingw --enable-threads --disable-nls --enable-languages=c,c++,fortran,objc,obj-c++,ada --disable-win32-registry --enable-sjlj-exceptions --enable-libstdcxx-debug --enable-cxx-flags=-fno-function-sections -fno-data-sections --enable-version-specific-runtime-libs --disable-bootstrap
Thread model: win32
gcc version 4.2.1-sjlj (mingw32-2)
 c:/rtools/mingw/bin/../libexec/gcc/mingw32/4.2.1-sjlj/cc1.exe -quiet -v -Ie:/biocbld/bbs-2.6-bioc/R/include -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava -iprefix c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/ -D_R_ -DWin32 RSJava/ErrorHandling.c -quiet -dumpbase ErrorHandling.c -mtune=generic -march=i486 -auxbase-strip RSJava/ErrorHandling.o -O3 -Wall -std=gnu99 -version -o e:\biocbld\bbs-2.6-bioc\tmpdir/cch1Q3Az.s
ignoring nonexistent directory "c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/include"
ignoring nonexistent directory "/mingw/include"
ignoring nonexistent directory "/mingw/lib/gcc/mingw32/4.2.1-sjlj/include"
ignoring nonexistent directory "/mingw/mingw32/include"
ignoring nonexistent directory "/mingw/include"
#include "..." search starts here:
#include <...> search starts here:
 e:/biocbld/bbs-2.6-bioc/R/include
 C:/JDK/jdk1.6.0_16/include
 C:/JDK/jdk1.6.0_16/include/win32
 e:/biocbld/bbs-2.6-bioc/R/include
 e:/biocbld/bbs-2.6-bioc/R/include/R_ext
 ../inst/include
 ../src/RSJava
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/include
End of search list.
GNU C version 4.2.1-sjlj (mingw32-2) (mingw32)
	compiled by GNU C version 4.2.1 (mingw32-dw2-1).
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 5a206dd7daa613ab6fd5107577c565b8
 c:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/bin/as.exe -o RSJava/ErrorHandling.o e:\biocbld\bbs-2.6-bioc\tmpdir/cch1Q3Az.s
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -D_R_ -DWin32 -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava    -v   -O3 -Wall  -std=gnu99 -c RSJava/ManagerInterfaceUtils.c -o RSJava/ManagerInterfaceUtils.o
Using built-in specs.
Target: mingw32
Configured with: ../gcc-4.2.1-2-src/configure --with-gcc --enable-libgomp --host=mingw32 --build=mingw32 --target=mingw32 --program-suffix=-sjlj --with-arch=i486 --with-tune=generic --disable-werror --prefix=/mingw --with-local-prefix=/mingw --enable-threads --disable-nls --enable-languages=c,c++,fortran,objc,obj-c++,ada --disable-win32-registry --enable-sjlj-exceptions --enable-libstdcxx-debug --enable-cxx-flags=-fno-function-sections -fno-data-sections --enable-version-specific-runtime-libs --disable-bootstrap
Thread model: win32
gcc version 4.2.1-sjlj (mingw32-2)
 c:/rtools/mingw/bin/../libexec/gcc/mingw32/4.2.1-sjlj/cc1.exe -quiet -v -Ie:/biocbld/bbs-2.6-bioc/R/include -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava -iprefix c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/ -D_R_ -DWin32 RSJava/ManagerInterfaceUtils.c -quiet -dumpbase ManagerInterfaceUtils.c -mtune=generic -march=i486 -auxbase-strip RSJava/ManagerInterfaceUtils.o -O3 -Wall -std=gnu99 -version -o e:\biocbld\bbs-2.6-bioc\tmpdir/ccXYh4DM.s
ignoring nonexistent directory "c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/include"
ignoring nonexistent directory "/mingw/include"
ignoring nonexistent directory "/mingw/lib/gcc/mingw32/4.2.1-sjlj/include"
ignoring nonexistent directory "/mingw/mingw32/include"
ignoring nonexistent directory "/mingw/include"
#include "..." search starts here:
#include <...> search starts here:
 e:/biocbld/bbs-2.6-bioc/R/include
 C:/JDK/jdk1.6.0_16/include
 C:/JDK/jdk1.6.0_16/include/win32
 e:/biocbld/bbs-2.6-bioc/R/include
 e:/biocbld/bbs-2.6-bioc/R/include/R_ext
 ../inst/include
 ../src/RSJava
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/include
End of search list.
GNU C version 4.2.1-sjlj (mingw32-2) (mingw32)
	compiled by GNU C version 4.2.1 (mingw32-dw2-1).
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 5a206dd7daa613ab6fd5107577c565b8
 c:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/bin/as.exe -o RSJava/ManagerInterfaceUtils.o e:\biocbld\bbs-2.6-bioc\tmpdir/ccXYh4DM.s
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -D_R_ -DWin32 -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava    -v   -O3 -Wall  -std=gnu99 -c RSJava/References.c -o RSJava/References.o
Using built-in specs.
Target: mingw32
Configured with: ../gcc-4.2.1-2-src/configure --with-gcc --enable-libgomp --host=mingw32 --build=mingw32 --target=mingw32 --program-suffix=-sjlj --with-arch=i486 --with-tune=generic --disable-werror --prefix=/mingw --with-local-prefix=/mingw --enable-threads --disable-nls --enable-languages=c,c++,fortran,objc,obj-c++,ada --disable-win32-registry --enable-sjlj-exceptions --enable-libstdcxx-debug --enable-cxx-flags=-fno-function-sections -fno-data-sections --enable-version-specific-runtime-libs --disable-bootstrap
Thread model: win32
gcc version 4.2.1-sjlj (mingw32-2)
 c:/rtools/mingw/bin/../libexec/gcc/mingw32/4.2.1-sjlj/cc1.exe -quiet -v -Ie:/biocbld/bbs-2.6-bioc/R/include -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava -iprefix c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/ -D_R_ -DWin32 RSJava/References.c -quiet -dumpbase References.c -mtune=generic -march=i486 -auxbase-strip RSJava/References.o -O3 -Wall -std=gnu99 -version -o e:\biocbld\bbs-2.6-bioc\tmpdir/ccvgyVj1.s
ignoring nonexistent directory "c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/include"
ignoring nonexistent directory "/mingw/include"
ignoring nonexistent directory "/mingw/lib/gcc/mingw32/4.2.1-sjlj/include"
ignoring nonexistent directory "/mingw/mingw32/include"
ignoring nonexistent directory "/mingw/include"
#include "..." search starts here:
#include <...> search starts here:
 e:/biocbld/bbs-2.6-bioc/R/include
 C:/JDK/jdk1.6.0_16/include
 C:/JDK/jdk1.6.0_16/include/win32
 e:/biocbld/bbs-2.6-bioc/R/include
 e:/biocbld/bbs-2.6-bioc/R/include/R_ext
 ../inst/include
 ../src/RSJava
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/include
End of search list.
GNU C version 4.2.1-sjlj (mingw32-2) (mingw32)
	compiled by GNU C version 4.2.1 (mingw32-dw2-1).
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 5a206dd7daa613ab6fd5107577c565b8
 c:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/bin/as.exe -o RSJava/References.o e:\biocbld\bbs-2.6-bioc\tmpdir/ccvgyVj1.s
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -D_R_ -DWin32 -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava    -v   -O3 -Wall  -std=gnu99 -c RSJava/JNIUtils.c -o RSJava/JNIUtils.o
Using built-in specs.
Target: mingw32
Configured with: ../gcc-4.2.1-2-src/configure --with-gcc --enable-libgomp --host=mingw32 --build=mingw32 --target=mingw32 --program-suffix=-sjlj --with-arch=i486 --with-tune=generic --disable-werror --prefix=/mingw --with-local-prefix=/mingw --enable-threads --disable-nls --enable-languages=c,c++,fortran,objc,obj-c++,ada --disable-win32-registry --enable-sjlj-exceptions --enable-libstdcxx-debug --enable-cxx-flags=-fno-function-sections -fno-data-sections --enable-version-specific-runtime-libs --disable-bootstrap
Thread model: win32
gcc version 4.2.1-sjlj (mingw32-2)
 c:/rtools/mingw/bin/../libexec/gcc/mingw32/4.2.1-sjlj/cc1.exe -quiet -v -Ie:/biocbld/bbs-2.6-bioc/R/include -IC:/JDK/jdk1.6.0_16/include -IC:/JDK/jdk1.6.0_16/include/win32 -Ie:/biocbld/bbs-2.6-bioc/R/include -Ie:/biocbld/bbs-2.6-bioc/R/include/R_ext -I../inst/include -I../src/RSJava -iprefix c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/ -D_R_ -DWin32 RSJava/JNIUtils.c -quiet -dumpbase JNIUtils.c -mtune=generic -march=i486 -auxbase-strip RSJava/JNIUtils.o -O3 -Wall -std=gnu99 -version -o e:\biocbld\bbs-2.6-bioc\tmpdir/ccdfucCd.s
ignoring nonexistent directory "c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/include"
ignoring nonexistent directory "/mingw/include"
ignoring nonexistent directory "/mingw/lib/gcc/mingw32/4.2.1-sjlj/include"
ignoring nonexistent directory "/mingw/mingw32/include"
ignoring nonexistent directory "/mingw/include"
#include "..." search starts here:
#include <...> search starts here:
 e:/biocbld/bbs-2.6-bioc/R/include
 C:/JDK/jdk1.6.0_16/include
 C:/JDK/jdk1.6.0_16/include/win32
 e:/biocbld/bbs-2.6-bioc/R/include
 e:/biocbld/bbs-2.6-bioc/R/include/R_ext
 ../inst/include
 ../src/RSJava
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include
 c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/include
End of search list.
GNU C version 4.2.1-sjlj (mingw32-2) (mingw32)
	compiled by GNU C version 4.2.1 (mingw32-dw2-1).
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 5a206dd7daa613ab6fd5107577c565b8
 c:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/bin/as.exe -o RSJava/JNIUtils.o e:\biocbld\bbs-2.6-bioc\tmpdir/ccdfucCd.s
gcc -shared -s -o SJava.dll tmp.def 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 -D_JNI_IMPLEMENTATION_ -Wl,--kill-at -LC:/JDK/jdk1.6.0_16/lib -LC:/JDK/jdk1.6.0_16/jre/bin/server -ljvm -Le:/biocbld/bbs-2.6-bioc/R/bin -lR
Info: resolving _R_CStackLimit by linking to __imp__R_CStackLimit (auto-import)
Info: resolving _R_Interactive by linking to __imp__R_Interactive (auto-importc:/rtools/mingw/bin/../lib/gcc/mingw32/4.2.1-sjlj/../../../../mingw32/bin/ld.exe: warning: auto-importing has been activated without --enable-auto-import specified on the command line.
This should work unless it involves constant data structures referencing symbols from auto-imported DLLs.)

cp SJava.dll RInterpreter.dll
  ... done
** R
** inst
** preparing package for lazy loading
Creating a new generic function for "merge" in "SJava"
** help
*** installing help indices
** building package indices ...
** MD5 sums
* DONE (SJava)