Package: Rgraphviz

Version: 1.13.4

Command: /loc/biocbuild/2.0d/R/bin/R CMD build Rgraphviz

RetCode: 1

Time: 10.1 seconds

Status: ERROR

PackageFile: None

* checking for file 'Rgraphviz/DESCRIPTION' ... OK
* preparing 'Rgraphviz':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'Rgraphviz' ...
checking for pkg-config... /usr/local/bin/pkg-config
sh: gnome-config: not 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: pkg-config was not able to find graphviz.  Verify graphviz is installed and that PKG_CONFIG_PATH is correct.
checking for dotneato-config... /usr/local/bin/dotneato-config
configure: Found graphviz 2.2.1
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_2_2_TO_2_3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c LL_funcs.c -o LL_funcs.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:17,
                 from LL_funcs.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from LL_funcs.c:1:
/loc/biocbuild/2.0d/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
LL_funcs.c: In function 'Rgraphviz_getDefAttrsGraph':
LL_funcs.c:67: warning: unused variable 'at_val'
LL_funcs.c:67: warning: unused variable 'at_name'
LL_funcs.c: In function 'Rgraphviz_setAttrsGraph':
LL_funcs.c:121: warning: implicit declaration of function 'agsafeset'
LL_funcs.c: In function 'Rgraphviz_toFile':
LL_funcs.c:445: warning: implicit declaration of function 'gvLayout'
LL_funcs.c:447: warning: implicit declaration of function 'gvRenderFilename'
LL_funcs.c:449: warning: implicit declaration of function 'gvFreeLayout'
LL_funcs.c:449: warning: unused variable 'i3'
LL_funcs.c:447: warning: unused variable 'i2'
LL_funcs.c:445: warning: unused variable 'i1'
LL_funcs.c: In function 'Rgraphviz_getDefAttrsEdge':
LL_funcs.c:368: warning: 'val' may be used uninitialized in this function
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_2_2_TO_2_3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c Rgraphviz.c -o Rgraphviz.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:17,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from Rgraphviz.c:1:
/loc/biocbuild/2.0d/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_2_2_TO_2_3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c RgraphvizInit.c -o RgraphvizInit.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:17,
                 from RgraphvizInit.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from RgraphvizInit.c:1:
/loc/biocbuild/2.0d/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_2_2_TO_2_3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c agopen.c -o agopen.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:17,
                 from agopen.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from agopen.c:1:
/loc/biocbuild/2.0d/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_2_2_TO_2_3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c agread.c -o agread.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:17,
                 from agread.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from agread.c:1:
/loc/biocbuild/2.0d/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_2_2_TO_2_3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c agwrite.c -o agwrite.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:17,
                 from agwrite.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from agwrite.c:1:
/loc/biocbuild/2.0d/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_2_2_TO_2_3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c bezier.c -o bezier.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:17,
                 from bezier.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from bezier.c:1:
/loc/biocbuild/2.0d/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_2_2_TO_2_3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c buildEdgeList.c -o buildEdgeList.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:17,
                 from buildEdgeList.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from buildEdgeList.c:1:
/loc/biocbuild/2.0d/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_2_2_TO_2_3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c buildNodeList.c -o buildNodeList.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:17,
                 from buildNodeList.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from buildNodeList.c:1:
/loc/biocbuild/2.0d/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_2_2_TO_2_3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c doLayout.c -o doLayout.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:17,
                 from doLayout.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from doLayout.c:1:
/loc/biocbuild/2.0d/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
doLayout.c: In function 'Rgraphviz_doLayout':
doLayout.c:330: warning: implicit declaration of function 'gvLayout'
doLayout.c:330: error: 'layouts' undeclared (first use in this function)
doLayout.c:330: error: (Each undeclared identifier is reported only once
doLayout.c:330: error: for each function it appears in.)
make: *** [doLayout.o] Error 1
chmod: getting attributes of `/tmp/Rinst2131070778/Rgraphviz/libs/*': No such file or directory
ERROR: compilation failed for package 'Rgraphviz'
** Removing '/tmp/Rinst2131070778/Rgraphviz'
 ERROR
Installation failed.
Removing '/tmp/Rinst2131070778'