[BioC] Failed installing SJava on MacOS
Martin Morgan
mtmorgan at fhcrc.org
Tue Jan 19 17:58:57 CET 2010
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/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"
My javaConfig() (not on Mac) has ${OMEGA_HOME} expanded
Slot "properties":
EmbeddedInR
"true"
InterfaceManagerClass
"org/omegahat/Interfaces/NativeInterface/OmegaInterfaceManager"
ForeignReferenceBaseClass
"org/omegahat/R/Java/RJavaInstance"
java.compiler
"NONE"
OMEGA_HOME
"/home/mtmorgan/arch/x86_64/R-devel/library/SJava/org/omegahat"
OmegahatSearchPath
".,/home/mtmorgan/arch/x86_64/R-devel/library/SJava/org/omegahat/Environment/Scripts/Run,/home/mtmorgan/arch/x86_64/R-devel/library/SJava/org/omegahat/Jars/Environment.jar"
java.library.path
"/home/mtmorgan/arch/x86_64/R-devel/library/SJava/libs"
> java.library.path
> "/Library/Frameworks/R.framework/Resources/library/SJava/libs"
>
> Slot "options":
> character(0)
>
> Slot "args":
> character(0)
>
>
>
>
>
>
>
>
>
>
>>> During installation I got the following error message, which I suspect to be relevant:
>>>
>>> ...
>>> ** R
>>> ** inst
>>> cp: cannot overwrite directory /Library/Frameworks/R.framework/Resources/library/SJava/libs with non-directory inst/libs
>>> sh: /usr/bin/tarxf: No such file or directory
>>> ....
>>>
>>> I also manually copied src/SJava.so to /Library/Frameworks/R.framework/Resources/library/SJava/libs but that didn't change anything.
>>> I put the full output of javareconf, R CMD INSTALL, and sessionInfo() here. Any help would be appreciated.
>>>
>>> Michael
>>>
>>>
>>>
>>> ========================================================================================================
>>>
>>> Seneca:compile mdondrup$ R CMD javareconf
>>> Java interpreter : /System/Library/Frameworks/JavaVM.framework/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
>>>
>>> _______________________________________________
>>> 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
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