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Re: [igraph] Problem installing igraph R package on 64-bit Mac Pro

From: Michael Braun
Subject: Re: [igraph] Problem installing igraph R package on 64-bit Mac Pro
Date: Tue, 10 Feb 2009 12:55:45 -0500 
Gabor:
As requested, here is the complete output. I did try installing the precompiled binary from CRAN, but got a message "Error: package 'igraph' is not installed for 'arch=x86_64' " when trying to load the library (of course, it works fine on a 32-bit build). 

Michael



> install.packages("igraph",type="source")
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/igraph_0.5.1.tar.gz'
Content type 'application/x-gzip' length 1040752 bytes (1016 Kb)
opened URL
==================================================
downloaded 1016 Kb

* Installing *source* package 'igraph' ...
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 g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for fmemopen... no
checking for open_memstream... no
checking for rintf... yes
checking for finite... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking for xml2-config... /usr/bin/xml2-config
checking for xmlSAXUserParseFile in -lxml2... yes
checking libxml/parser.h usability... yes
checking libxml/parser.h presence... yes
checking for libxml/parser.h... yes
checking for __gmpz_add in -lgmp... no
configure: creating ./config.status
config.status: creating src/config.h
config.status: creating R/config.R
config.status: creating src/Makevars
** libs
** arch - x86_64
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/ usr/local/include -I/usr/local/include/apophenia -I/usr/local/ include -DUSING_R -fPIC -g -O2 -c DensityGrid.cpp -o DensityGrid.o g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/ usr/local/include -I/usr/local/include/apophenia -I/usr/local/ include -DUSING_R -fPIC -g -O2 -c NetDataTypes.cpp -o NetDataTypes.o g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/ usr/local/include -I/usr/local/include/apophenia -I/usr/local/ include -DUSING_R -fPIC -g -O2 -c NetRoutines.cpp -o NetRoutines.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c adjlist.c -o adjlist.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c arpack.c -o arpack.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c array.c -o array.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c atlas.c -o atlas.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c attributes.c -o attributes.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c basic_query.c -o basic_query.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c bfgs.c -o bfgs.o g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/ usr/local/include -I/usr/local/include/apophenia -I/usr/local/ include -DUSING_R -fPIC -g -O2 -c bliss.cc -o bliss.o g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/ usr/local/include -I/usr/local/include/apophenia -I/usr/local/ include -DUSING_R -fPIC -g -O2 -c bliss_eqrefhash.cc -o bliss_eqrefhash.o g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/ usr/local/include -I/usr/local/include/apophenia -I/usr/local/ include -DUSING_R -fPIC -g -O2 -c bliss_graph.cc -o bliss_graph.o g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/ usr/local/include -I/usr/local/include/apophenia -I/usr/local/ include -DUSING_R -fPIC -g -O2 -c bliss_heap.cc -o bliss_heap.o g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/ usr/local/include -I/usr/local/include/apophenia -I/usr/local/ include -DUSING_R -fPIC -g -O2 -c bliss_orbit.cc -o bliss_orbit.o g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/ usr/local/include -I/usr/local/include/apophenia -I/usr/local/ include -DUSING_R -fPIC -g -O2 -c bliss_partition.cc -o bliss_partition.o g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/ usr/local/include -I/usr/local/include/apophenia -I/usr/local/ include -DUSING_R -fPIC -g -O2 -c bliss_timer.cc -o bliss_timer.o g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/ usr/local/include -I/usr/local/include/apophenia -I/usr/local/ include -DUSING_R -fPIC -g -O2 -c bliss_utils.cc -o bliss_utils.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c cattributes.c -o cattributes.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c centrality.c -o centrality.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c cliques.c -o cliques.o g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/ usr/local/include -I/usr/local/include/apophenia -I/usr/local/ include -DUSING_R -fPIC -g -O2 -c clustertool.cpp -o clustertool.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c cocitation.c -o cocitation.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c community.c -o community.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c components.c -o components.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c conversion.c -o conversion.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c cores.c -o cores.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c d_lg10.c -o d_lg10.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c d_sign.c -o d_sign.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dasum.c -o dasum.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c daxpy.c -o daxpy.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dcopy.c -o dcopy.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c ddot.c -o ddot.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dgemv.c -o dgemv.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dgeqr2.c -o dgeqr2.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dger.c -o dger.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dgetv0.c -o dgetv0.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlabad.c -o dlabad.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlacon.c -o dlacon.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlacpy.c -o dlacpy.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dladiv.c -o dladiv.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlae2.c -o dlae2.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlaev2.c -o dlaev2.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlaexc.c -o dlaexc.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlahqr.c -o dlahqr.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlaln2.c -o dlaln2.o gcc-4.2 -arch x86_64 -std=gnu99 -Wall -O3 -g -p -pg -DHAVE_INLINE - fPIC -ffloat-store -c dlamch.c 
dlamch.c: In function ‘dlamc2_’:
dlamch.c:656: warning: format ‘%8i’ expects type ‘int’, but argument 2 has type ‘integer’ 
dlamch.c: At top level:
dlamch.c:398: warning: ‘c__1’ defined but not used
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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlange.c -o dlange.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlanhs.c -o dlanhs.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlanst.c -o dlanst.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlanv2.c -o dlanv2.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlapy2.c -o dlapy2.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlaqrb.c -o dlaqrb.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlarf.c -o dlarf.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlarfg.c -o dlarfg.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlarfx.c -o dlarfx.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlarnv.c -o dlarnv.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlartg.c -o dlartg.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlaruv.c -o dlaruv.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlascl.c -o dlascl.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlaset.c -o dlaset.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlasr.c -o dlasr.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlasrt.c -o dlasrt.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlassq.c -o dlassq.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dlasy2.c -o dlasy2.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dmout.c -o dmout.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dnaitr.c -o dnaitr.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dnapps.c -o dnapps.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dnaup2.c -o dnaup2.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dnaupd.c -o dnaupd.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dnconv.c -o dnconv.o 
dnconv.c:23: warning: ‘debug_’ defined but not used
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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dneigh.c -o dneigh.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dneupd.c -o dneupd.o 
dneupd.c:33: warning: ‘timing_’ defined but not used
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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dngets.c -o dngets.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dnrm2.c -o dnrm2.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dorm2r.c -o dorm2r.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dqueue.c -o dqueue.o g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/ usr/local/include -I/usr/local/include/apophenia -I/usr/local/ include -DUSING_R -fPIC -g -O2 -c drl_graph.cpp -o drl_graph.o g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/ usr/local/include -I/usr/local/include/apophenia -I/usr/local/ include -DUSING_R -fPIC -g -O2 -c drl_layout.cpp -o drl_layout.o g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/ usr/local/include -I/usr/local/include/apophenia -I/usr/local/ include -DUSING_R -fPIC -g -O2 -c drl_parse.cpp -o drl_parse.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c drot.c -o drot.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dsaitr.c -o dsaitr.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dsapps.c -o dsapps.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dsaup2.c -o dsaup2.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dsaupd.c -o dsaupd.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dscal.c -o dscal.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dsconv.c -o dsconv.o 
dsconv.c:23: warning: ‘debug_’ defined but not used
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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dseigt.c -o dseigt.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dsesrt.c -o dsesrt.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dseupd.c -o dseupd.o 
dseupd.c:33: warning: ‘timing_’ defined but not used
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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dsgets.c -o dsgets.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dsortc.c -o dsortc.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dsortr.c -o dsortr.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dstatn.c -o dstatn.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dstats.c -o dstats.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dsteqr.c -o dsteqr.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dstqrb.c -o dstqrb.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dswap.c -o dswap.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dtrevc.c -o dtrevc.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dtrexc.c -o dtrexc.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dtrmm.c -o dtrmm.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dtrsen.c -o dtrsen.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dtrsyl.c -o dtrsyl.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c dvout.c -o dvout.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c error.c -o error.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c etime_.c -o etime_.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c evolver_cit.c -o evolver_cit.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c fast_community.c -o fast_community.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c flow.c -o flow.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c foreign-gml-lexer.c -o foreign-gml-lexer.o 
foreign-gml-lexer.c:1182: warning: ‘yyunput’ defined but not used
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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c foreign-gml-parser.c -o foreign-gml-parser.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c foreign-graphml.c -o foreign-graphml.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c foreign-lgl-lexer.c -o foreign-lgl-lexer.o 
foreign-lgl-lexer.c:1142: warning: ‘yyunput’ defined but not used
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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c foreign-lgl-parser.c -o foreign-lgl-parser.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c foreign-ncol-lexer.c -o foreign-ncol-lexer.o 
foreign-ncol-lexer.c:1136: warning: ‘yyunput’ defined but not used
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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c foreign-ncol-parser.c -o foreign-ncol-parser.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c foreign-pajek-lexer.c -o foreign-pajek-lexer.o 
foreign-pajek-lexer.c:1594: warning: ‘yyunput’ defined but not used
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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c foreign-pajek-parser.c -o foreign-pajek-parser.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 -I/usr/local/include/apophenia -I/usr/ local/include -Wall -O3 -g -p -pg -DHAVE_INLINE -fPIC -Wall -O3 -g -p -pg -DHAVE_INLINE -c foreign.c -o foreign.o 
foreign.c: In function ‘igraph_write_graph_gml’:
foreign.c:2367: error: ‘PACKAGE_VERSION’ undeclared (first use in this function) 
foreign.c:2367: error: (Each undeclared identifier is reported only once
foreign.c:2367: error: for each function it appears in.)
foreign.c: In function ‘igraph_write_graph_dot’:
foreign.c:2603: error: ‘PACKAGE_VERSION’ undeclared (first use in this function) 
make: *** [foreign.o] Error 1
chmod: /Library/Frameworks/R.framework/Resources/library/igraph/libs/ x86_64/*: No such file or directory 
ERROR: compilation failed for package 'igraph'
** Removing '/Library/Frameworks/R.framework/Resources/library/igraph'
** Restoring previous '/Library/Frameworks/R.framework/Resources/ library/igraph' 

The downloaded packages are in
/private/var/folders/6g/6gqJUHG-FsGAUUywFq+B3U++q3w/-Tmp-/Rtmp551Mkq/ downloaded_packages 
Updating HTML index of packages in '.Library'
Warning message:
In install.packages("igraph", type = "source") :
  installation of package 'igraph' had non-zero exit status






On Feb 10, 2009, at 12:30 PM, Gábor Csárdi wrote:


This is not easy to solve, because I don't have a mac and Apple does
not let us run OSX in a virtual machine....

On Tue, Feb 10, 2009 at 4:33 PM, Michael Braun <address@hidden> wrote:

I was using

install.packages("igraph",type="source")
from wtihin R. I just tried R CMD INSTALL igraph from the bash shell, and 
got the same result.


Could you send the whole output? I suspect that ./configure is not
even run on your system, I don't know why....


I also installed the gmp library, and got the same problem.


For the GMP version to work, you need to install the binary version of
the package. You tried that? Check the igraph.so file in the package,
perhaps you have 'ldd' on OSX, that tells to which dynamic libraries
igraph links to and whether your linker is able to find them.

G.

ps. Please stay on the list, just to make the archive more useful.
Thanks. Btw. if you don't sign up, you might miss some answers,
because they are normally sent only to the list.


On Feb 10, 2009, at 10:28 AM, Gábor Csárdi wrote:


Michael, the error message for the binary package means that it was
compiled with the GMP library. (See http://gmp.darwinports.com/)
Perhaps if you install that, then it will be fine.

The R package is usually compiled without this library, so I don't
know why this wasn't the case for the one you downloaded.

The compilation failure is also strange a bit, it looks like R is
ignoring some configuration files in the package. Just to be sure, you 
did the compilation with

R CMD INSTALL igraph_0.5.1.tar.gz

right?

G.
On Tue, Feb 10, 2009 at 4:07 PM, Michael Braun <address@hidden> wrote:
Hi. First, thank you for creating and maintaining the igraph R package. 
I
use it quite often and find it to be very usefull.
However, I am having trouble installing a 64-bit version in R. If I 
install
the binary, downloaded from CRAN, and then load it, I get:


install.packages("igraph",repos="http://stat.cmu.edu/R/CRAN";)


trying URL

'http://stat.cmu.edu/R/CRAN/bin/macosx/leopard/contrib/2.8/igraph_0.5.1.tgz'
Content type 'application/x-gzip' length 3058038 bytes (2.9 Mb)
opened URL
==================================================
downloaded 2.9 Mb


The downloaded packages are in
/var/folders/6g/6gqJUHG-FsGAUUywFq+B3U++q3w/-Tmp-//RtmpmuFm5c/ downloaded_packages 

library(igraph)


Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/Library/Frameworks/R.framework/Resources/library/igraph/libs/ x86_64/igraph.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/igraph/ libs/x86_64/igraph.so, 
10): Symbol not found: ___gmpz_clear
Referenced from:
/Library/Frameworks/R.framework/Resources/library/igraph/libs/ x86_64/igraph.so 
Expected in: dynamic lookup

Error : .onLoad failed in 'loadNamespace' for 'igraph'
Error: package/namespace load failed for 'igraph'







If I try to compile from source, I eventually get:

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 -I/usr/local/include/apophenia -I/usr/local/ include 
-Wall -O3 -g -p -pg -DHAVE_INLINE  -fPIC  -Wall -O3 -g -p -pg
-DHAVE_INLINE
-c foreign.c -o foreign.o
foreign.c: In function 'igraph_write_graph_gml':
foreign.c:2367: error: 'PACKAGE_VERSION' undeclared (first use in this 
function)
foreign.c:2367: error: (Each undeclared identifier is reported only once 
foreign.c:2367: error: for each function it appears in.)
foreign.c: In function 'igraph_write_graph_dot':
foreign.c:2603: error: 'PACKAGE_VERSION' undeclared (first use in this 
function)
make: *** [foreign.o] Error 1
chmod:
/Library/Frameworks/R.framework/Resources/library/igraph/libs/ x86_64/*: 
No
such file or directory
ERROR: compilation failed for package 'igraph'
** Removing '/Library/Frameworks/R.framework/Resources/library/ igraph' 
** Restoring previous
'/Library/Frameworks/R.framework/Resources/library/igraph'

I have no problems with a 32-bit R build.
By the way, I have an Intel-based Mac Pro, running Leopard (10.5.6). The 
R
version is 2.8.0.
Ideally, I'd just want to install the binary, but neither approach seems 
to
work.

Can you help?

Thanks,

Michael







-------------------------------------------
Michael Braun
Homer A. Burnell Career Development Professor, and
    Assistant Professor of Management Science (Marketing Group)
MIT Sloan School of Management
One Amherst St., E40-169
Cambridge, MA 02142
address@hidden
617-253-3436






_______________________________________________
igraph-help mailing list
address@hidden
http://lists.nongnu.org/mailman/listinfo/igraph-help





--
Gabor Csardi <address@hidden>     UNIL DGM


-------------------------------------------
Michael Braun
Homer A. Burnell Career Development Professor, and
      Assistant Professor of Management Science (Marketing Group)
MIT Sloan School of Management
One Amherst St., E40-169
Cambridge, MA 02142
address@hidden
617-253-3436









--
Gabor Csardi <address@hidden>     UNIL DGM


-------------------------------------------
Michael Braun
Homer A. Burnell Career Development Professor, and
        Assistant Professor of Management Science (Marketing Group)
MIT Sloan School of Management
One Amherst St., E40-169
Cambridge, MA 02142
address@hidden
617-253-3436
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