[BioC] Problems with installation of Rgraphviz

[jdmitrie at liacs.nl]

Dear Bioconductor developer,

During installation of Rgraphviz I get the following errors.


* Installing *source* package 'Rgraphviz' ...
checking for graphviz... checking for dotneato-config... not found
checking for pkg-config... /usr/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/lib/R/include -I/usr/lib/R/include -DGRAPHVIZGT_2_4
-I/usr/local/include   -fpic  -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -m32 -march=i386 -mtune=pentium4 -fasynchronous-unwind-tables
-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: syntax error before ‘*’ token
common.h:47: warning: data definition has no type or storage class
common.h:62: error: syntax error before ‘*’ token
common.h:63: error: syntax error before ‘*’ token
common.h:67: error: syntax error before ‘*’ token
common.h:68: error: syntax error before ‘*’ token
common.h:78: error: syntax error before ‘*’ token
common.h:78: error: syntax error before ‘*’ token
common.h:78: warning: data definition has no type or storage class
common.h:79: error: syntax error before ‘*’ token
common.h:79: error: syntax error before ‘*’ token
common.h:79: warning: data definition has no type or storage class
common.h:80: error: syntax error before ‘*’ token
common.h:80: error: syntax error before ‘*’ token
common.h:80: warning: data definition has no type or storage class
common.h:83: error: syntax error before ‘*’ token
common.h:83: error: syntax error before ‘*’ token
common.h:83: warning: data definition has no type or storage class
Rgraphviz.c: In function ‘Rgraphviz_init’:
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: warning: assignment makes pointer from integer without a cast
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: 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: 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: 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: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: error: ‘tmp’ undeclared (first use in this function)
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:191: error: syntax error before ‘)’ token
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: 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: At top level:
Rgraphviz.c:711: error: syntax error before ‘*’ token
Rgraphviz.c: In function ‘buildRagraph’:
Rgraphviz.c:714: error: ‘g’ undeclared (first use in this function)
Rgraphviz.c: At top level:
Rgraphviz.c:731: error: syntax error before ‘*’ token
Rgraphviz.c: In function ‘getBoundBox’:
Rgraphviz.c:743: error: ‘g’ undeclared (first use in this function)
Rgraphviz.c: At top level:
Rgraphviz.c:755: error: syntax error before ‘*’ token
Rgraphviz.c: In function ‘getNodeLayouts’:
Rgraphviz.c:756: error: ‘Agnode_t’ undeclared (first use in this function)
Rgraphviz.c:756: error: ‘node’ undeclared (first use in this function)
Rgraphviz.c:762: error: ‘g’ undeclared (first use in this function)
Rgraphviz.c:790: warning: passing argument 1 of ‘R_scalarString’ makes
pointer from integer without a cast
Rgraphviz.c:792: warning: passing argument 1 of ‘R_scalarString’ makes
pointer from integer without a cast
Rgraphviz.c:794: warning: passing argument 1 of ‘R_scalarString’ makes
pointer from integer without a cast
Rgraphviz.c:796: warning: passing argument 1 of ‘R_scalarString’ makes
pointer from integer without a cast
Rgraphviz.c: At top level:
Rgraphviz.c:839: error: syntax error before ‘*’ token
Rgraphviz.c: In function ‘getEdgeLocs’:
Rgraphviz.c:842: error: ‘Agnode_t’ undeclared (first use in this function)
Rgraphviz.c:842: error: ‘node’ undeclared (first use in this function)
Rgraphviz.c:842: error: ‘head’ undeclared (first use in this function)
Rgraphviz.c:843: error: ‘Agedge_t’ undeclared (first use in this function)
Rgraphviz.c:843: error: ‘edge’ undeclared (first use in this function)
Rgraphviz.c:845: error: ‘bezier’ undeclared (first use in this function)
Rgraphviz.c:845: error: syntax error before ‘bez’
Rgraphviz.c:860: error: ‘numEdges’ undeclared (first use in this function)
Rgraphviz.c:862: error: ‘g’ undeclared (first use in this function)
Rgraphviz.c:869: error: ‘bez’ undeclared (first use in this function)
Rgraphviz.c:917: warning: passing argument 1 of ‘R_scalarString’ makes
pointer from integer without a cast
Rgraphviz.c:919: warning: passing argument 1 of ‘R_scalarString’ makes
pointer from integer without a cast
Rgraphviz.c:921: warning: passing argument 1 of ‘R_scalarString’ makes
pointer from integer without a cast
Rgraphviz.c:924: warning: passing argument 1 of ‘R_scalarString’ makes
pointer from integer without a cast
Rgraphviz.c: In function ‘Rgraphviz_graphvizVersion’:
Rgraphviz.c:986: error: request for member ‘info’ in something not a
structure or union
Rgraphviz.c: At top level:
Rgraphviz.c:993: error: syntax error before ‘*’ token
Rgraphviz.c:993: error: syntax error before ‘*’ token
Rgraphviz.c: In function ‘setDefaultAttrs’:
Rgraphviz.c:1002: error: ‘attrs’ undeclared (first use in this function)
Rgraphviz.c:1006: error: ‘g’ undeclared (first use in this function)
make: *** [Rgraphviz.o] Error 1
chmod: cannot access `/usr/lib/R/library/Rgraphviz/libs/*': No such file
or directory
ERROR: compilation failed for package 'Rgraphviz'
** Removing '/usr/lib/R/library/Rgraphviz'

The downloaded packages are in
        /tmp/RtmpZc98B8/downloaded_packages
Warning message:
installation of package 'Rgraphviz' had non-zero exit status in:
install.packages("Rgraphviz")

I try to install Rgraphviz whith biocLite("Rgraphviz"),
also with install.packages("Rgraphviz"),
but the result is the same.

Can you help me.

Whith best regards,
Julia Dmitrieva