[BioC] Failed installing SJava on MacOS
Michael Dondrup
Michael.Dondrup at uni.no
Tue Jan 19 16:31:03 CET 2010
Am Jan 19, 2010 um 3:39 PM schrieb Martin Morgan:
> Michael Dondrup wrote:
>> Hi,
>> I would like to use RWebServices and therefore SJava on Mac OS snow leopard. The documentation does not explicitly mention Mac os, so it's
>> maybe not supported, but i hope it can be made working anyway.
>> Maybe somebody out there got this configuration running and could help? I am trying to install SJava 0.72. I try the following:
>>
>>> library(SJava)
>> Load the Java VM with .JavaInit()
>>> .JavaInit()
>>> example(.Java)
>>
>> .Java> v <- .JavaConstructor("java.util.Vector", as.integer(10))
>>
>> .Java> .Java(v, "add", "A string element")
>> Error in .Java(v, "add", "A string element") :
>> Can't find org.omegahat.R.Java.RForeignReference
>
> Hi Michael --
>
> .JavaInit has an argument default=javaConfig() which sets the class path
> and other variables. My guess is that javaConfig() needs to be augmented
> to return the correct class path. On my system it is
>
>> javaConfig()@classPath
> [1] "<...>/library/SJava/org/omegahat/Jars/Environment.jar"
> [2] "<...>/library/SJava/org/.."
> [3] "<...>/library/SJava/org/omegahat/Jars/antlr.jar"
> [4] "<...>/library/SJava/org/omegahat/Jars/jas.jar"
> [5] "<...>/library/SJava/org/omegahat/Jars/jhall.jar"
>
> where <...> is the path to my R installation.
>
> Martin
Hi Martin,
thank you very much for your reply. My configuration looks pretty much like yours. All jars exist and readable.
I tried messing around
with the paths in addition, adding "/Library/Frameworks/R.framework/Resources/library/SJava/org/" (without the ..), to no avail.
Are you using a Mac? It would be good to compare the full output of javaConfig() for a functioning version,
maybe you could send that to me?
And might be good to know in which jar the class org.omegahat.R.Java.RForeignReference is contained.
If that is relevant:
java version "1.6.0_17"
Java(TM) SE Runtime Environment (build 1.6.0_17-b04-248-10M3025)
Java HotSpot(TM) 64-Bit Server VM (build 14.3-b01-101, mixed mode)
Here is the output of javaConfig().
> javaConfig()
An object of class "JavaConfiguration"
Slot "classPath":
[1] "/Library/Frameworks/R.framework/Resources/library/SJava/org/omegahat/Jars/Environment.jar"
[2] "/Library/Frameworks/R.framework/Resources/library/SJava/org/.."
[3] "/Library/Frameworks/R.framework/Resources/library/SJava/org/omegahat/Jars/antlr.jar"
[4] "/Library/Frameworks/R.framework/Resources/library/SJava/org/omegahat/Jars/jas.jar"
[5] "/Library/Frameworks/R.framework/Resources/library/SJava/org/omegahat/Jars/jhall.jar"
Slot "libraryPath":
[1] "/Library/Frameworks/R.framework/Resources/library/SJava/libs"
Slot "properties":
EmbeddedInR
"true"
InterfaceManagerClass
"org/omegahat/Interfaces/NativeInterface/OmegaInterfaceManager"
ForeignReferenceBaseClass
"org/omegahat/R/Java/RJavaInstance"
java.compiler
"NONE"
OMEGA_HOME
"/Library/Frameworks/R.framework/Resources/library/SJava/org/omegahat"
OmegahatSearchPath
".,${OMEGA_HOME}/Environment/Scripts/Run,${OMEGA_HOME}/Jars/Environment.jar"
java.library.path
"/Library/Frameworks/R.framework/Resources/library/SJava/libs"
Slot "options":
character(0)
Slot "args":
character(0)
>
>
>>
>> During installation I got the following error message, which I suspect to be relevant:
>>
>> ...
>> ** R
>> ** inst
>> cp: cannot overwrite directory /Library/Frameworks/R.framework/Resources/library/SJava/libs with non-directory inst/libs
>> sh: /usr/bin/tarxf: No such file or directory
>> ....
>>
>> I also manually copied src/SJava.so to /Library/Frameworks/R.framework/Resources/library/SJava/libs but that didn't change anything.
>> I put the full output of javareconf, R CMD INSTALL, and sessionInfo() here. Any help would be appreciated.
>>
>> Michael
>>
>>
>>
>> ========================================================================================================
>>
>> Seneca:compile mdondrup$ R CMD javareconf
>> Java interpreter : /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/bin/java
>> Java version : 1.6.0_17
>> Java home path : /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home
>> Java compiler : /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/bin/javac
>> Java headers gen.: /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/bin/javah
>> Java archive tool: /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/bin/jar
>> Java library path:
>> JNI linker flags : -framework JavaVM
>> JNI cpp flags : -I$(JAVA_HOME)/include
>>
>> Updating Java configuration in /Library/Frameworks/R.framework/Resources
>> sed: -e: No such file or directory
>> sed: s|JAVA_CPPFLAGS =.\{0,\}|JAVA_CPPFLAGS = -I$(JAVA_HOME)/include|g: No such file or directory
>> sed: -e: No such file or directory
>> sed: s|JAVA_CPPFLAGS =.\{0,\}|JAVA_CPPFLAGS = -I$(JAVA_HOME)/include|g: No such file or directory
>> Done.
>>
>> Seneca:compile mdondrup$ sudo R CMD INSTALL -c SJava
>> Password:
>> * installing to library '/Library/Frameworks/R.framework/Resources/library'
>> * installing *source* package 'SJava' ...
>> checking shlib support in R... checking Java support in R... present:
>> interpreter : '/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/bin/java'
>> archiver : '/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/bin/jar'
>> compiler : '/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/bin/javac'
>> header prep.: '/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/bin/javah'
>> cpp flags : '-I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include'
>> java libs : '-framework JavaVM'
>> Looking in /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include
>> 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
>> ** arch - x86_64
>> /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/bin/javah -classpath /Users/mdondrup/compile/SJava/inst:/Users/mdondrup/compile/SJava/inst/org/omegahat/Jars/Environment.jar -o RForeignReference.h org.omegahat.R.Java.RForeignReference
>> /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/bin/javah -classpath /Users/mdondrup/compile/SJava/inst:/Users/mdondrup/compile/SJava/inst/org/omegahat/Jars/Environment.jar -o RManualFunctionActionListener.h org.omegahat.R.Java.RManualFunctionActionListener
>> /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/bin/javah -classpath /Users/mdondrup/compile/SJava/inst:/Users/mdondrup/compile/SJava/inst/org/omegahat/Jars/Environment.jar -o ROmegahatInterpreter.h org.omegahat.R.Java.ROmegahatInterpreter
>> /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/bin/javah -classpath /Users/mdondrup/compile/SJava/inst:/Users/mdondrup/compile/SJava/inst/org/omegahat/Jars/Environment.jar -o REvaluator.h org.omegahat.R.Java.REvaluator
>> make -C RSJava
>> /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/bin/javah -classpath /Users/mdondrup/compile/SJava/inst:/Users/mdondrup/compile/SJava/inst/org/omegahat/Jars/Environment.jar -o OmegaInterfaceManager.h \
>> org.omegahat.Interfaces.NativeInterface.OmegaInterfaceManager
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -fPIC -mtune=core2 -g -O2 -c CtoJava.c -o CtoJava.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -fPIC -mtune=core2 -g -O2 -c ErrorHandling.c -o ErrorHandling.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -fPIC -mtune=core2 -g -O2 -c ManagerInterfaceUtils.c -o ManagerInterfaceUtils.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -fPIC -mtune=core2 -g -O2 -c References.c -o References.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -fPIC -mtune=core2 -g -O2 -c JNIUtils.c -o JNIUtils.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o libRSNativeJava.so CtoJava.o ErrorHandling.o ManagerInterfaceUtils.o References.o JNIUtils.o -framework JavaVM
>> if test ! -d /Library/Frameworks/R.framework/Resources/library/SJava/libs ; then \
>> mkdir /Library/Frameworks/R.framework/Resources/library/SJava/libs ; \
>> fi
>> cp CtoJava.h ErrorHandling.h ManagerInterfaceUtils.h References.h JNIUtils.h /Users/mdondrup/compile/SJava/inst/include
>> mv libRSNativeJava.so /Users/mdondrup/compile/SJava/inst/libs
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c ConverterExamples.c -o ConverterExamples.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c Converters.c -o Converters.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c Reflectance.c -o Reflectance.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c REmbed.c -o REmbed.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c REmbedWin.c -o REmbedWin.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c REval.c -o REval.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c RFunctionListener.c -o RFunctionListener.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c RReferenceCall.c -o RReferenceCall.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c RStoJava.c -o RStoJava.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c RtoJava.c -o RtoJava.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c RSJava/CtoJava.c -o RSJava/CtoJava.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c RSJava/ErrorHandling.c -o RSJava/ErrorHandling.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c RSJava/ManagerInterfaceUtils.c -o RSJava/ManagerInterfaceUtils.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c RSJava/References.c -o RSJava/References.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -D_R_ -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/R_ext -I/Users/mdondrup/compile/SJava/src/RSJava -I. -I/Users/mdondrup/compile/SJava/inst/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/include -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c RSJava/JNIUtils.c -o RSJava/JNIUtils.o
>> gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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 -framework JavaVM -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
>> ln -s SJava.so /Library/Frameworks/R.framework/Resources/library/SJava/libs/libSJava.so
>> ln -s SJava.so /Library/Frameworks/R.framework/Resources/library/SJava/libs/libRInterpreter.so
>> ** R
>> ** inst
>> cp: cannot overwrite directory /Library/Frameworks/R.framework/Resources/library/SJava/libs with non-directory inst/libs
>> sh: /usr/bin/tarxf: No such file or directory
>> ** preparing package for lazy loading
>> Creating a new generic function for "merge" in "SJava"
>> ** help
>> *** installing help indices
>> ** building package indices ...
>> make -C RSJava -f Makefile clean
>> rm OmegaInterfaceManager.h
>> rm RForeignReference.h RManualFunctionActionListener.h ROmegahatInterpreter.h REvaluator.h
>> * DONE (SJava)
>>
>>
>>
>>
>>
>>
>>
>>
>>> sessionInfo()
>> R version 2.10.1 (2009-12-14)
>> x86_64-apple-darwin9.8.0
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] SJava_0.72.0
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.10.1
>>
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>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
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