[R-SIG-Mac] Failure to compile Rgraphviz on Mac OS X
Simon Urbanek
simon.urbanek at r-project.org
Thu Oct 18 18:31:34 CEST 2007
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
>>> 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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