[BioC] Failed installing SJava on MacOS
Martin Morgan
mtmorgan at fhcrc.org
Tue Jan 19 15:39:01 CET 2010
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
>
> 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
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PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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