[R-SIG-Mac] Failure to compile Rgraphviz on Mac OS X
Michael Kubovy
kubovy at virginia.edu
Thu Oct 18 18:07:47 CEST 2007
Hi Simon,
I reinstalled from binary. Then:
> 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
>> R-SIG-Mac at stat.math.ethz.ch
>> 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/
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