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jdmitrie@liacs.nl
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@jdmitrieliacsnl-1741
Last seen 9.8 years ago
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