JGR not working on Snow Leopard
It seems I have been able to install 64bit R. R version 2.9.2 Patched (2009-09-05 r49613) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [R.app GUI 1.28 (5399) x86_64-apple-darwin9.8.0] I could not, however, find a newer installer version of R.app (or R64.app) Trying to install JGR still does not work. I downloaded 64bit JGR as I was told, but on start it tells me it needs to install some additional libraries, and then tells ,e that it could not finish its work. the JGR packages is missing. So I try 188-23-83-195:devel neuwirth$ sudo R --arch x86_64 CMD INSTALL JGR * Installing to library ?/Library/Frameworks/R.framework/Resources/ library? * Installing *source* package ?JGR? ... ** R ** inst ** preparing package for lazy loading Error in library(CarbonEL) : there is no package called 'CarbonEL' Error : package 'iplots' could not be loaded ERROR: lazy loading failed for package ?JGR? * Removing ?/Library/Frameworks/R.framework/Resources/library/JGR? 188-23-83-195:devel neuwirth$ How can I get past this problem?
On Sep 11, 2009, at 4:19 PM, Simon Urbanek wrote:
Erich, On Sep 11, 2009, at 9:08 AM, Erich Neuwirth wrote:
I am experiencing problems with JGR on Snow Leopard.
Apple only provides 64-bit Java in Snow Leopard, so you can only use 64-bit R. In addition, you'll need 64-bit JGR launcher which you can download from http://urbanek.info/JGR-1.6-SL.dmg (despite the name it is compatible with both JGR 1.6 and 1.7 [I tested is with the latter]) (When installing packages from sources for 64-bir R, please make sure you use --arch x86_64 to build the 64-bit version). Cheers, Simon
After looking for similar messaged I found that I should start JGR from the command line. Further down is the output. I also rebuilt rJava from the source package and this did not help. JGR gives me an error message: Cannot find Java/R (JR) library (libjri.jnilib) Please make sure you start by double clicking the JGR application. 91-115-197-166:~ neuwirth$ /Applications/JGR.app/Contents/MacOS/ JGRLoading preferences from /Users/neuwirth/.JGRprefsrcJGR R_HOME: / Library/Frameworks/R.framework/Resourceslibroot: /Library/ Frameworks/R.framework/Resources/library/Attempting to load jnilib: /Library/Frameworks/R.framework/Resources/library/rJava/jri/ libjri.jnilib Succeeded in loading jnilib, looks good. JGR DYLD_LIBRARY_PATH: /Library/Frameworks/R.framework/Resources/ library/rJava/jri Loading class file... result -1 RCP: JGR CLASSPATH: -Drjava.class.path=/Applications/JGR.app:/Library/ Frameworks/R.framework/Resources/library/rJava/jri/JRI.jar:/Library/ Frameworks/R.framework/Resources/library/iplots/java/iplots.jar:/ Library/Frameworks/R.framework/Resources/library/JGR/java/JGR.jar R_ARCH=/i386 arguments to java: java -cp /Library/Frameworks/R.framework/Resources/library/rJava/java/boot -Xmx512m -Xdock:icon=/Applications/JGR.app/Contents/Resources/JGR.icns -Dapple.laf.useScreenMenuBar=true -Dcom.apple.mrj.application.apple.menu.about.name=JGR -Dmain.class=org.rosuda.JGR.JGR -Djgr.loader.ver=1.61 -Djgr.load.pkgs=yes -Drjava.class.path=/Applications/JGR.app:/Library/Frameworks/ R.framework/Resources/library/rJava/jri/JRI.jar:/Library/Frameworks/ R.framework/Resources/library/iplots/java/iplots.jar:/Library/ Frameworks/R.framework/Resources/library/JGR/java/JGR.jar -Drjava.path=/Library/Frameworks/R.framework/Resources/library/rJava RJavaClassLoader On Sep 11, 2009, at 2:25 AM, Simon Urbanek wrote:
Peter, you have probably compiled ncl in 64-bit (default on SL) but you're using 32-bit R, so it won't work. Either use 64-bit R or compile ncl for 32-bit. Cheers, Simon On Sep 10, 2009, at 7:58 PM, Peter Cowan wrote:
I'm running 10.6 from clean install, with the supplied Xcode, and R 2.9.2. I am unable to build a package (specifically the phylobase package [1]) which built fine under 10.5.8. Even more confusingly it seems to build fine for others using 10.6. The end of the install log (appended below) contains the these potentially informative errors: ld: warning: in ncl/ncl/.libs/libncl.a, file is not of required architecture ld: warning: duplicate dylib /usr/local/lib/libgcc_s.1.dylib The latter error I get with any source package, but doesn't seem to prevent them from being installed. The package also makes use of the Rcpp interface to use an included library (NCL). It is this included library that seems to not build correctly, which could very well be related to the old version of Rcpp, or the makefiles responsible for building it. I've tried all manner of tweaking, upgrading, and list searching, but the (probably obvious) solution still eludes me. Any pointers in the right direction are greatly appreciated. Peter [1] https://r-forge.r-project.org/projects/phylobase/ =========================
sessionInfo()
R version 2.9.2 (2009-08-24) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base ========================= birch$ which gfortran /usr/local/bin/gfortran birch$ gfortran --version GNU Fortran (GCC) 4.2.3 Copyright (C) 2007 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING ============================ * Installing to library ?/Library/Frameworks/R.framework/ Resources/library? * Installing *source* package ?phylobase? ... 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 g++ -arch i386 accepts -g... yes checking how to run the C++ preprocessor... g++ -arch i386 -E Building libRcpp.a in RcppSrc... g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c Rcpp.cpp -o Rcpp.o ar crs libRcpp.a Rcpp.o g++ --version i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5646) Copyright (C) 2007 Free Software Foundation, Inc. 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(cached) yes configure: creating ./config.status config.status: creating Makefile config.status: creating ncl/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands make all-recursive Making all in ncl /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsassumptionsblock.lo -MD - MP -MF .deps/nxsassumptionsblock.Tpo -c -o nxsassumptionsblock.lo nxsassumptionsblock.cpp mkdir .libs g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsassumptionsblock.lo -MD -MP -MF .deps/nxsassumptionsblock.Tpo -c nxsassumptionsblock.cpp -fno-common -DPIC -o .libs/nxsassumptionsblock.o g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsassumptionsblock.lo -MD -MP -MF .deps/nxsassumptionsblock.Tpo -c nxsassumptionsblock.cpp -o nxsassumptionsblock.o >/dev/null 2>&1 mv -f .deps/nxsassumptionsblock.Tpo .deps/nxsassumptionsblock.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsblock.lo -MD -MP -MF .deps/nxsblock.Tpo -c -o nxsblock.lo nxsblock.cpp g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsblock.lo -MD -MP -MF .deps/nxsblock.Tpo -c nxsblock.cpp -fno-common -DPIC -o .libs/nxsblock.o g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsblock.lo -MD -MP -MF .deps/nxsblock.Tpo -c nxsblock.cpp -o nxsblock.o
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string
constant to 'char*'
g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT
nxsunalignedblock.lo -MD -MP -MF .deps/nxsunalignedblock.Tpo -c
nxsunalignedblock.cpp -o nxsunalignedblock.o >/dev/null 2>&1
mv -f .deps/nxsunalignedblock.Tpo .deps/nxsunalignedblock.Plo
/bin/sh ../libtool --tag=CXX --mode=link g++ -O3 -ffast-math -
fPIC
-release 2.0.04 -o libncl.la -rpath /usr/local/lib/ncl
nxsassumptionsblock.lo nxsblock.lo nxscharactersblock.lo
nxsdatablock.lo nxsdiscretedatum.lo nxsdiscretematrix.lo
nxsdistancedatum.lo nxsdistancesblock.lo nxsexception.lo
nxsreader.lo
nxssetreader.lo nxsstring.lo nxstaxablock.lo nxstoken.lo
nxstreesblock.lo nxsunalignedblock.lo
g++ -dynamiclib -single_module ${wl}-flat_namespace ${wl}-undefined
${wl}suppress -o .libs/libncl-2.0.04 .libs/nxsassumptionsblock.o
.libs/nxsblock.o .libs/nxscharactersblock.o .libs/nxsdatablock.o
.libs/nxsdiscretedatum.o .libs/nxsdiscretematrix.o
.libs/nxsdistancedatum.o .libs/nxsdistancesblock.o
.libs/nxsexception.o .libs/nxsreader.o .libs/nxssetreader.o
.libs/nxsstring.o .libs/nxstaxablock.o .libs/nxstoken.o
.libs/nxstreesblock.o .libs/nxsunalignedblock.o -install_name
/usr/local/lib/ncl/libncl-2.0.04
(cd .libs && rm -f libncl && ln -s libncl-2.0.04 libncl)
ar cru .libs/libncl.a nxsassumptionsblock.o nxsblock.o
nxscharactersblock.o nxsdatablock.o nxsdiscretedatum.o
nxsdiscretematrix.o nxsdistancedatum.o nxsdistancesblock.o
nxsexception.o nxsreader.o nxssetreader.o nxsstring.o
nxstaxablock.o
nxstoken.o nxstreesblock.o nxsunalignedblock.o
ranlib .libs/libncl.a
creating libncl.la
(cd .libs && rm -f libncl.la && ln -s ../libncl.la libncl.la)
configure: creating ./config.status
config.status: creating src/Makevars
** libs
** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386
-I/usr/local/include -IRcppSrc -Incl/ncl -fPIC -g -O2 -c
NCLInterface.cpp -o NCLInterface.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386
-I/usr/local/include -IRcppSrc -Incl/ncl -fPIC -g -O2 -c
ReadWithNCL.cpp -o ReadWithNCL.o
gcc -arch i386 -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386
-I/usr/local/include -fPIC -g -O2 -c descendants.c -o
descendants.o
gcc -arch i386 -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386
-I/usr/local/include -fPIC -g -O2 -c reorderBinary.c -o
reorderBinary.o
gcc -arch i386 -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386
-I/usr/local/include -fPIC -g -O2 -c reorderRobust.c -o
reorderRobust.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names
-mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module
-multiply_defined suppress -L/usr/local/lib -o phylobase.so
NCLInterface.o ReadWithNCL.o descendants.o reorderBinary.o
reorderRobust.o -LRcppSrc -lRcpp -Lncl/ncl/.libs -lncl
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
ld: warning: in ncl/ncl/.libs/libncl.a, file is not of required
architecture
ld: warning: duplicate dylib /usr/local/lib/libgcc_s.1.dylib
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "summary" in "phylobase"
Creating a new generic function for "plot" in "phylobase"
** help
*** installing help indices
Building/Updating help pages for package 'phylobase'
Formats: text html latex example addData text html latex example as-methods text html latex example check.phylo4 text html latex extract.tree text html latex example formatData text html latex geospiza text html latex example hasSingles text html latex example multiPhylo-class text html latex example pdata-class text html latex pdata text html latex phylo4-accessors text html latex example Note: removing empty section \usage in file 'phylo4-class.Rd' Note: removing empty section \value in file 'phylo4-class.Rd' Note: removing empty section \arguments in file 'phylo4-class.Rd' Note: removing empty section \examples in file 'phylo4-class.Rd' phylo4-class text html latex phylo4-display text html latex example phylo4-labels text html latex example phylo4 text html latex example Note: removing empty section \usage in file 'phylo4d-class.Rd' Note: removing empty section \value in file 'phylo4d-class.Rd' phylo4d-class text html latex example Note: removing empty section \examples in file 'phylo4d-display.Rd' phylo4d-display text html latex phylo4d-hasData text html latex example phylo4d text html latex example phyloXXYY text html latex example phylobase-package text html latex phylobubbles text html latex example phylog text html latex phylomat-class text html latex example plotOneTree text html latex example printphylo4 text html latex example read.nexustreestring text html latex readNexus text html latex reorder-methods text html latex example subset-methods text html latex example tdata text html latex example tip.data.plot text html latex treePlot-methods text html latex example treewalk text html latex example ** building package indices ... * DONE (phylobase)
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