Michael Dondrup wrote: > 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 this is in org.omegahat/Jars/RJava.jar, e.g., jar tf org.omegahat/Jars/RJava.jar more below... >> 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/ome gahat/Jars/Environment.jar" > [2] "/Library/Frameworks/R.framework/Resources/library/SJava/org/.." > [3] "/Library/Frameworks/R.framework/Resources/library/SJava/org/ome gahat/Jars/antlr.jar" > [4] "/Library/Frameworks/R.framework/Resources/library/SJava/org/ome gahat/Jars/jas.jar" > [5] "/Library/Frameworks/R.framework/Resources/library/SJava/org/ome gahat/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/Environm ent.jar" My javaConfig() (not on Mac) has ${OMEGA_HOME} expanded Slot "properties": EmbeddedInR "true" InterfaceManagerClass "org/omegahat/Interfaces/NativeInterface/OmegaInterfaceManager" ForeignReferenceBaseClass "org/omegahat/R/Java/RJavaInstance" java.compiler "NONE" OMEGA_HOME "/home/mtmorgan/arch/x86_64/R-devel/library/SJava/org/omegahat" OmegahatSearchPath ".,/home/mtmorgan/arch/x86_64/R-devel/library/SJava/org/omegahat/Envir onment/Scripts/Run,/home/mtmorgan/arch/x86_64/R-devel/library/SJava/or g/omegahat/Jars/Environment.jar" java.library.path "/home/mtmorgan/arch/x86_64/R-devel/library/SJava/libs" > java.library.path > "/Library/Frameworks/R.framework/Resources/library/SJava/libs" > > Slot "options": > character(0) > > Slot "args": > character(0) > > > > > > > > > > >>> During installation I got the following error message, which I suspect to be relevant: >>> >>> ... >>> ** R >>> ** inst >>> cp: cannot overwrite directory /Library/Frameworks/R.framework/Resources/library/SJava/libs with non- directory inst/libs >>> sh: /usr/bin/tarxf: No such file or directory >>> .... >>> >>> I also manually copied src/SJava.so to /Library/Frameworks/R.framework/Resources/library/SJava/libs but that didn't change anything. >>> I put the full output of javareconf, R CMD INSTALL, and sessionInfo() here. Any help would be appreciated. >>> >>> Michael >>> >>> >>> >>> ================================================================== ====================================== >>> >>> Seneca:compile mdondrup$ R CMD javareconf >>> Java interpreter : /System/Library/Frameworks/JavaVM.framework/Ver sions/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/Ver sions/CurrentJDK/Home/bin/javac >>> Java headers gen.: /System/Library/Frameworks/JavaVM.framework/Ver sions/CurrentJDK/Home/bin/javah >>> Java archive tool: /System/Library/Frameworks/JavaVM.framework/Ver sions/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/Version s/CurrentJDK/Home/bin/java' >>> archiver : '/System/Library/Frameworks/JavaVM.framework/Version s/CurrentJDK/Home/bin/jar' >>> compiler : '/System/Library/Frameworks/JavaVM.framework/Version s/CurrentJDK/Home/bin/javac' >>> header prep.: '/System/Library/Frameworks/JavaVM.framework/Version s/CurrentJDK/Home/bin/javah' >>> cpp flags : '-I/System/Library/Frameworks/JavaVM.framework/Versi ons/CurrentJDK/Home/include' >>> java libs : '-framework JavaVM' >>> Looking in /System/Library/Frameworks/JavaVM.framework/Versions/Cu rrentJDK/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/Ho me/bin/javah -classpath /Users/mdondrup/compile/SJava/inst:/Users/mdon drup/compile/SJava/inst/org/omegahat/Jars/Environment.jar -o RForeignReference.h org.omegahat.R.Java.RForeignReference >>> /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Ho me/bin/javah -classpath /Users/mdondrup/compile/SJava/inst:/Users/mdon drup/compile/SJava/inst/org/omegahat/Jars/Environment.jar -o RManualFunctionActionListener.h org.omegahat.R.Java.RManualFunctionActionListener >>> /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Ho me/bin/javah -classpath /Users/mdondrup/compile/SJava/inst:/Users/mdon drup/compile/SJava/inst/org/omegahat/Jars/Environment.jar -o ROmegahatInterpreter.h org.omegahat.R.Java.ROmegahatInterpreter >>> /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Ho me/bin/javah -classpath /Users/mdondrup/compile/SJava/inst:/Users/mdon drup/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/Ho me/bin/javah -classpath /Users/mdondrup/compile/SJava/inst:/Users/mdon drup/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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/Framew orks/JavaVM.framework/Versions/CurrentJDK/Home/include -I/System/Libra ry/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/includ e -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/S Java/libs/libSJava.so >>> ln -s SJava.so /Library/Frameworks/R.framework/Resources/library/S Java/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 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> -- >> 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 > -- 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