[BioC] installing Rgraphviz on FC5

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Hi Stefan,

Make sure that graphviz has been installed from the rpm and not
compiled from source. Installing from rpms, when possible, makes
life with Fedora _much_ simpler.
The rpms your need to install are:
  graphviz
  graphviz-devel
Both are available from the Fedora Extras repository.
See the "Unofficial Fedora FAQ" ( http://www.fedorafaq.org/ )
for how to install stuff from the Fedora Extras repos... and for
many other very usefull tips.
Cheers,

H.


Stefan Schmidt wrote:
> Dear all,
>
>  
>
> I am new to this mailing list and I am only just starting to use linux.
>
> On trying to install Rgraphviz on my system (FC5, on a dual opteron system)
> I get the below error message. I checked that graphviz is istalled on the
> system. Please, does anyone know what I doing wrong here (and what I should
> do instead) ?
>
> Thanks for your help,
>
>  
>
> Stefan.
>
>  
>
> * Installing *source* package 'Rgraphviz' ...
>
> checking for graphviz... checking for dotneato-config... not found
>
> checking for pkg-config... /usr/local/bin/pkg-config
>
> Package libgvc was not found in the pkg-config search path.
>
> Perhaps you should add the directory containing `libgvc.pc'
>
> to the PKG_CONFIG_PATH environment variable
>
> No package 'libgvc' found
>
> Package libgvc was not found in the pkg-config search path.
>
> Perhaps you should add the directory containing `libgvc.pc'
>
> to the PKG_CONFIG_PATH environment variable
>
> No package 'libgvc' found
>
> configure: creating ./config.status
>
> config.status: creating src/Makevars
>
> ** libs
>
> gcc -I/usr/lib64/R/include -I/usr/lib64/R/include -DGRAPHVIZGT_2_4
> -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
> -c Rgraphviz.c -o Rgraphviz.o
>
> In file included from Rgraphviz.c:1:
>
> common.h:26:17: error: gvc.h: No such file or directory
>
> common.h:27:22: error: gvplugin.h: No such file or directory
>
> common.h:28:20: error: gvcext.h: No such file or directory
>
> common.h:29:20: error: gvcint.h: No such file or directory
>
> common.h:30:21: error: globals.h: No such file or directory
>
> In file included from Rgraphviz.c:1:
>
> common.h:47: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
>
> common.h:62: error: expected ')' before '*' token
>
> common.h:63: error: expected ')' before '*' token
>
> common.h:67: error: expected ')' before '*' token
>
> common.h:68: error: expected ')' before '*' token
>
> common.h:78: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
>
> common.h:79: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
>
> common.h:80: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
>
> common.h:83: error: expected '=', ',', ';', 'asm' or '__attribute__' before
> '*' token
>
> Rgraphviz.c: In function 'Rgraphviz_init':
>
> Rgraphviz.c:92: warning: implicit declaration of function 'agseterr'
>
> Rgraphviz.c:92: error: 'AGERR' undeclared (first use in this function)
>
> Rgraphviz.c:92: error: (Each undeclared identifier is reported only once
>
> Rgraphviz.c:92: error: for each function it appears in.)
>
> Rgraphviz.c:98: error: 'gvc' undeclared (first use in this function)
>
> Rgraphviz.c:98: warning: implicit declaration of function 'gvContext'
>
> Rgraphviz.c: In function 'Rgraphviz_fin':
>
> Rgraphviz.c:108: error: 'Agraph_t' undeclared (first use in this function)
>
> Rgraphviz.c:108: error: 'g' undeclared (first use in this function)
>
> Rgraphviz.c:112: warning: implicit declaration of function 'agclose'
>
> Rgraphviz.c: In function 'Rgraphviz_agread':
>
> Rgraphviz.c:119: error: 'Agraph_t' undeclared (first use in this function)
>
> Rgraphviz.c:119: error: 'g' undeclared (first use in this function)
>
> Rgraphviz.c:126: warning: implicit declaration of function 'aginit'
>
> Rgraphviz.c:127: warning: implicit declaration of function 'agread'
>
> Rgraphviz.c:129: warning: implicit declaration of function 'buildRagraph'
>
> Rgraphviz.c:129: warning: return makes pointer from integer without a cast
>
> Rgraphviz.c: In function 'Rgraphviz_agwrite':
>
> Rgraphviz.c:134: error: 'Agraph_t' undeclared (first use in this function)
>
> Rgraphviz.c:134: error: 'g' undeclared (first use in this function)
>
> Rgraphviz.c:148: warning: implicit declaration of function 'agwrite'
>
> Rgraphviz.c: In function 'Rgraphviz_agopen':
>
> Rgraphviz.c:159: error: 'Agraph_t' undeclared (first use in this function)
>
> Rgraphviz.c:159: error: 'g' undeclared (first use in this function)
>
> Rgraphviz.c:159: error: 'tmpGraph' undeclared (first use in this function)
>
> Rgraphviz.c:159: warning: left-hand operand of comma expression has no
> effect
>
> Rgraphviz.c:159: warning: statement with no effect
>
> Rgraphviz.c:160: error: 'sgs' undeclared (first use in this function)
>
> Rgraphviz.c:161: error: 'Agnode_t' undeclared (first use in this function)
>
> Rgraphviz.c:161: error: 'head' undeclared (first use in this function)
>
> Rgraphviz.c:161: error: 'tail' undeclared (first use in this function)
>
> Rgraphviz.c:161: warning: left-hand operand of comma expression has no
> effect
>
> Rgraphviz.c:161: error: 'tmp' undeclared (first use in this function)
>
> Rgraphviz.c:161: warning: left-hand operand of comma expression has no
> effect
>
> Rgraphviz.c:161: warning: statement with no effect
>
> Rgraphviz.c:162: error: 'Agedge_t' undeclared (first use in this function)
>
> Rgraphviz.c:162: error: 'curEdge' undeclared (first use in this function)
>
> Rgraphviz.c:185: warning: implicit declaration of function 'agopen'
>
> Rgraphviz.c:188: warning: implicit declaration of function 'setDefaultAttrs'
>
> Rgraphviz.c:191: error: expected expression before ')' token
>
> Rgraphviz.c:209: warning: implicit declaration of function 'agsubg'
>
> Rgraphviz.c:218: warning: implicit declaration of function 'agset'
>
> Rgraphviz.c:241: warning: implicit declaration of function 'agnode'
>
> Rgraphviz.c:266: warning: implicit declaration of function 'agfindnode'
>
> Rgraphviz.c:276: warning: implicit declaration of function 'agedge'
>
> Rgraphviz.c:292: warning: return makes pointer from integer without a cast
>
> Rgraphviz.c: In function 'Rgraphviz_getAttr':
>
> Rgraphviz.c:296: error: 'Agraph_t' undeclared (first use in this function)
>
> Rgraphviz.c:296: error: 'g' undeclared (first use in this function)
>
> Rgraphviz.c:304: warning: implicit declaration of function 'agget'
>
> Rgraphviz.c:304: warning: passing argument 1 of 'R_scalarString' makes
> pointer from integer without a cast
>
> Rgraphviz.c: In function 'Rgraphviz_doLayout':
>
> Rgraphviz.c:387: error: 'Agraph_t' undeclared (first use in this function)
>
> Rgraphviz.c:387: error: 'g' undeclared (first use in this function)
>
> Rgraphviz.c:429: warning: implicit declaration of function 'gvLayout'
>
> Rgraphviz.c:429: error: 'gvc' undeclared (first use in this function)
>
> Rgraphviz.c:435: warning: implicit declaration of function 'getNodeLayouts'
>
> Rgraphviz.c:435: warning: assignment makes pointer from integer without a
> cast
>
> Rgraphviz.c:436: warning: implicit declaration of function 'getBoundBox'
>
> Rgraphviz.c:436: warning: assignment makes pointer from integer without a
> cast
>
> Rgraphviz.c:437: warning: implicit declaration of function 'getEdgeLocs'
>
> Rgraphviz.c:437: warning: assignment makes pointer from integer without a
> cast
>
> Rgraphviz.c: At top level:
>
> Rgraphviz.c:711: error: expected ')' before '*' token
>
> Rgraphviz.c:731: error: expected ')' before '*' token
>
> Rgraphviz.c:755: error: expected ')' before '*' token
>
> Rgraphviz.c:839: error: expected ')' before '*' token
>
> Rgraphviz.c: In function 'Rgraphviz_graphvizVersion':
>
> Rgraphviz.c:986: error: 'gvc' undeclared (first use in this function)
>
> Rgraphviz.c: At top level:
>
> Rgraphviz.c:993: error: expected '=', ',', ';', 'asm' or '__attribute__'
> before '*' token
>
> make: *** [Rgraphviz.o] Error 1
>
> chmod: cannot access `/usr/lib64/R/library/Rgraphviz/libs/*': No such file
> or directory
>
> ERROR: compilation failed for package 'Rgraphviz'
>
> ** Removing '/usr/lib64/R/library/Rgraphviz'
>
>  
>
> Stefan Schmidt, MD
>
> Tyrolean Cancer Research Institute
>
> Innrain 66
>
> A-6020 Innsbruck
>
> Austria
>
>  
>
> phone: 0043-512-570485-15
>
> mail: Stefan.Schmidt at i-med.ac.at
>
>  
>
>
> 	[[alternative HTML version deleted]]
>
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>   


-- 
------------------------
Hervé Pagès
E-mail: hpages at fhcrc.org
 Phone: (206) 667-5791
   Fax: (206) 667-1319