Failure to compile Rgraphviz on Mac OS X

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