[R-SIG-Mac] Failure to compile Rgraphviz on Mac OS X

Simon Urbanek simon.urbanek at r-project.org
Thu Oct 18 17:09:47 CEST 2007 

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/
>
> _______________________________________________
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