hi stefan

it seems that you are not using the correct pkg-config bin which should be
located at /usr/bin/pkg-config, not at /usr/local/bin/pkg-config. try to
overwrite the PATH variable in the current console (with export
PATH=/usr/bin) and retry to install the source package from Rgraphviz
(always in the same console) with R CMD INSTALL Rgraphviz<version>.tar.gz

best, jo

On 7/11/06, Herve Pages <hpages@fhcrc.org> wrote:
>
> 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@i-med.ac.at
> >
> >
> >
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
>
> --
> ------------------------
> Hervé Pagès
> E-mail: hpages@fhcrc.org
> Phone: (206) 667-5791
>    Fax: (206) 667-1319
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
Johannes Rainer, Msc
Tyrolean Cancer Research Institute
Innrain 66, 6020 Innsbruck, Austria
Tel.: +43 512 570485 15
Email: johannes.rainer@tcri.at
          johannes.rainer@tugraz.at

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