[R-SIG-Mac] Failure to compile Rgraphviz on Mac OS X
Michael Kubovy
kubovy at virginia.edu
Fri Oct 19 02:03:44 CEST 2007
Thanks Simon,
Installing the binary rather than compiling and installing a new
Graphviz binary did the trick.
On Oct 18, 2007, at 12:31 PM, Simon Urbanek wrote:
>
> 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/
>>
>>
>>
_____________________________
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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