On Oct 18, 2007, at 12:07 PM, Michael Kubovy wrote: > Hi Simon, > > I reinstalled from binary. Then: >
Have you installed the corresponding Graphviz binary? (from http://r.research.att.com/) Cheers, Simon > > library(Rgraphviz) > Loading required package: graph > Error in dyn.load(file, ...) : > unable to load shared library '/Library/Frameworks/R.framework/ > Versions/2.6/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so': > dlopen(/Library/Frameworks/R.framework/Versions/2.6/Resources/ > library/Rgraphviz/libs/i386/Rgraphviz.so, 6): Library not loaded: / > usr/local/lib/libgvc.3.dylib > Referenced from: /Library/Frameworks/R.framework/Versions/2.6/ > Resources/library/Rgraphviz/libs/i386/Rgraphviz.so > Reason: image not found > Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz' > Error: package/namespace load failed for 'Rgraphviz' > > On Oct 18, 2007, at 11:09 AM, Simon Urbanek wrote: > >> Michael, >> >> your Graphviz-dev setup seems to be broken - look at your "Fount >> graphiviz..." output. >> Just out of curiosity - is the BioC binary of Rgraphviz not working >> for you? >> >> Cheers, >> Simon >> >> On Oct 18, 2007, at 10:52 AM, Michael Kubovy wrote: >> >>> Here is what the console says when I ask it to compile Rgraphviz: >>> >>> WARNING: ignoring environment value of R_HOME >>> * Installing *source* package 'Rgraphviz' ... >>> configure: No --with-graphviz option was specified. Trying to find >>> graphviz using other methods. >>> checking for pkg-config... no >>> configure: Using dotneato-config to find graphviz >>> checking for dotneato-config... no >>> configure: dotneato-config not found in PATH. >>> configure: Trying default graphviz dir /usr/local. Consider >>> specifying --with-graphviz >>> configure: Using graphviz root directory /usr/local >>> configure: Found graphviz not >>> Referenced >>> Reason: >>> configure: We have inferred the following flags for graphviz >>> configure: ..PKG_CPPFLAGS=-I/usr/local/include/graphviz >>> configure: ..PKG_LIBS=-L/usr/local/lib/graphviz -L/usr/local/lib - >>> lgvc >>> checking for whether compiler has bool... checking for gcc... gcc >>> ./configure: line 1459: test: too many arguments >>> ./configure: line 1481: test: too many arguments >>> ./configure: line 1481: test: too many arguments >>> 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 ANSI C... none needed >>> checking how to run the C preprocessor... gcc -E >>> checking for egrep... grep -E >>> checking for ANSI C header files... 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 for stdbool.h that conforms to C99... yes >>> checking for _Bool... yes >>> yes >>> configure: creating ./config.status >>> config.status: creating src/Makevars >>> ** libs >>> ** arch - i386 >>> >>> The downloaded packages are in >>> /private/tmp/RtmpkHbLv7/downloaded_packages >>> gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk - >>> std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/ >>> Resources/ >>> include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/ >>> usr/local/include/graphviz -DGRAPHVIZ_MAJOR=not Referenced >>> Reason: - >>> DGRAPHVIZ_MINOR=not Referenced Reason: -DHAVE_STDBOOL_H=1 - >>> DHAVE_BOOL=1 -msse3 -fPIC -g -O2 -march=nocona -c LL_funcs.c -o >>> LL_funcs.o >>> i686-apple-darwin8-gcc-4.0.1: Referenced: No such file or directory >>> i686-apple-darwin8-gcc-4.0.1: Reason:: No such file or directory >>> i686-apple-darwin8-gcc-4.0.1: Referenced: No such file or directory >>> i686-apple-darwin8-gcc-4.0.1: Reason:: No such file or directory >>> In file included from LL_funcs.c:1: >>> common.h:52: error: parse error before ‘*’ token >>> common.h:52: warning: type defaults to ‘int’ in declaration of >>> ‘agdictof’ >>> common.h:52: warning: data definition has no type or storage class >>> common.h:60: error: parse error before ‘*’ token >>> common.h:60: warning: type defaults to ‘int’ in declaration of ‘gvc’ >>> common.h:60: warning: data definition has no type or storage class >>> In file included from LL_funcs.c:2: >>> util.h:18: error: parse error before ‘*’ token >>> LL_funcs.c:5: error: parse error before ‘*’ token >>> LL_funcs.c:6: warning: return type defaults to ‘int’ >>> LL_funcs.c: In function ‘getAgraphPtr’: >>> LL_funcs.c:9: error: ‘Agraph_t’ undeclared (first use in this >>> function) >>> LL_funcs.c:9: error: (Each undeclared identifier is reported only >>> once >>> LL_funcs.c:9: error: for each function it appears in.) >>> LL_funcs.c:9: error: ‘g’ undeclared (first use in this function) >>> LL_funcs.c: At top level: >>> LL_funcs.c:15: error: parse error before ‘*’ token >>> LL_funcs.c:16: warning: return type defaults to ‘int’ >>> LL_funcs.c: In function ‘getClusterPtr’: >>> LL_funcs.c:17: error: ‘Agraph_t’ undeclared (first use in this >>> function) >>> LL_funcs.c:17: error: ‘g’ undeclared (first use in this function) >>> LL_funcs.c:24: error: ‘sg’ undeclared (first use in this function) >>> LL_funcs.c:24: warning: implicit declaration of function >>> ‘agfindsubg’ >>> LL_funcs.c: In function ‘getDefAttrs’: >>> LL_funcs.c:31: error: ‘Agdict_t’ undeclared (first use in this >>> function) >>> LL_funcs.c:31: error: ‘dict’ undeclared (first use in this function) >>> LL_funcs.c:34: warning: implicit declaration of function ‘dtsize’ >>> LL_funcs.c: In function ‘Rgraphviz_getDefAttrsGraph’: >>> LL_funcs.c:86: error: ‘Agraph_t’ ** Removing '/Library/Frameworks/ >>> R.framework/Versions/2.6/Resources/library/Rgraphviz' >>> ** Restoring previous '/Library/Frameworks/R.framework/Versions/2.6/ >>> Resources/library/Rgraphviz' >>> undeclared (first use in this function) >>> LL_funcs.c:86: error: ‘g’ undeclared (first use in this function) >>> LL_funcs.c: In function ‘Rgraphviz_setDefAttrsGraph’: >>> LL_funcs.c:113: error: ‘Agraph_t’ undeclared (first use in this >>> function) >>> LL_funcs.c:113: error: ‘g’ undeclared (first use in this function) >>> LL_funcs.c:118: error: ‘Agsym_t’ undeclared (first use in this >>> function) >>> LL_funcs.c:118: error: ‘r’ undeclared (first use in this function) >>> LL_funcs.c:118: warning: implicit declaration of function >>> ‘agraphattr’ >>> LL_funcs.c: In function ‘Rgraphviz_getAttrsGraph’: >>> LL_funcs.c:130: error: ‘Agraph_t’ undeclared (first use in this >>> function) >>> LL_funcs.c:130: error: ‘g’ undeclared (first use in this function) >>> LL_funcs.c:134: warning: implicit declaration of function ‘agget’ >>> LL_funcs.c:134: warning: initialization makes pointer from integer >>> without a cast >>> LL_funcs.c: In function ‘Rgraphviz_setAttrsGraph’: >>> LL_funcs.c:154: error: ‘Agraph_t’ undeclared (first use in this >>> function) >>> LL_funcs.c:154: error: ‘g’ undeclared (first use in this function) >>> LL_funcs.c:161: warning: implicit declaration of function >>> ‘agsafeset’ >>> LL_funcs.c: In function ‘Rgraphviz_getAttrsCluster’: >>> LL_funcs.c:173: error: ‘Agraph_t’ undeclared (first use in this >>> function) >>> LL_funcs.c:173: error: ‘sg’ undeclared (first use in this function) >>> LL_funcs.c:177: warning: initialization makes pointer from integer >>> without a cast >>> LL_funcs.c: In function ‘Rgraphviz_setAttrsCluster’: >>> LL_funcs.c:197: error: ‘Agraph_t’ undeclared (first use in this >>> function) >>> LL_funcs.c:197: error: ‘sg’ undeclared (first use in this function) >>> LL_funcs.c: In function ‘Rgraphviz_getDefAttrsNode’: >>> LL_funcs.c:216: error: ‘Agraph_t’ undeclared (first use in this >>> function) >>> LL_funcs.c:216: error: ‘g’ undeclared (first use in this function) >>> LL_funcs.c:219: error: ‘Agnode_t’ undeclared (first use in this >>> function) >>> LL_funcs.c:219: error: ‘n’ undeclared (first use in this function) >>> LL_funcs.c: In functionc:465: error: ‘curEdge’ undeclared (first use >>> in this function) >>> LL_funcs.c:490: warning: implicit declaration of function ‘aginit’ >>> LL_funcs.c:492: warning: implicit declaration of function ‘agopen’ >>> LL_funcs.c:496: error: parse error before ‘)’ token >>> LL_funcs.c:510: warning: implicit declaration of function ‘agsubg’ >>> LL_funcs.c:535: warning: implicit declaration of function ‘agnode’ >>> LL_funcs.c:565: warning: implicit declaration of function ‘agedge’ >>> make: *** [LL_funcs.o] Error 1 >>> chmod: /Library/Frameworks/R.framework/Versions/2.6/Resources/ >>> library/ >>> Rgraphviz/libs/i386/*: No such file or directory >>> ERROR: compilation failed for package 'Rgraphviz' >>> >>>> sessionInfo() >>> R version 2.6.0 (2007-10-03) >>> i386-apple-darwin8.10.1 >>> >>> locale: >>> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] graph_1.15.6 >>> >>> loaded via a namespace (and not attached): >>> [1] cluster_1.11.9 tools_2.6.0 >>> Warning message: >>> In install.packages(c("Rgraphviz"), lib = "/Library/Frameworks/ >>> R.framework/Resources/library/", : >>> installation of package 'Rgraphviz' had non-zero exit status >>> >>> _____________________________ >>> Professor Michael Kubovy >>> University of Virginia >>> Department of Psychology >>> USPS: P.O.Box 400400 Charlottesville, VA 22904-4400 >>> Parcels: Room 102 Gilmer Hall >>> McCormick Road Charlottesville, VA 22903 >>> Office: B011 +1-434-982-4729 >>> Lab: B019 +1-434-982-4751 >>> Fax: +1-434-982-4766 >>> WWW: http://www.people.virginia.edu/~mk9y/ >>> >>> _______________________________________________ >>> R-SIG-Mac mailing list >>> [email protected] >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >>> > > _____________________________ > Professor Michael Kubovy > University of Virginia > Department of Psychology > USPS: P.O.Box 400400 Charlottesville, VA 22904-4400 > Parcels: Room 102 Gilmer Hall > McCormick Road Charlottesville, VA 22903 > Office: B011 +1-434-982-4729 > Lab: B019 +1-434-982-4751 > Fax: +1-434-982-4766 > WWW: http://www.people.virginia.edu/~mk9y/ > > > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
