1.13.4Jeff Gentry | Linux (SUSE 9.2) | x86_64 | [ ERROR ] | skipped | |
| Linux (SUSE 10.1) | x86_64 | OK | WARNINGS | |
| Linux (SUSE 9.2) | i686 | ERROR | skipped | |
| Solaris 2.9 | sparc | ERROR | skipped | |
| Windows Server 2003 | x86_64 | ERROR | skipped | skipped |
| Windows Server 2003 | NA | ERROR | skipped | skipped |
| Mac OS X (10.4.6) | i686 | OK | ERROR | |
* 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/bin/pkg-config
configure: Found graphviz 2.8
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_4_TO_2_9 -I/usr/local/include -fpic -g -O2 -Wall -c agopen.c -o agopen.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz -DGRAPHVIZ_2_4_TO_2_9 -I/usr/local/include -fpic -g -O2 -Wall -c agread.c -o agread.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz -DGRAPHVIZ_2_4_TO_2_9 -I/usr/local/include -fpic -g -O2 -Wall -c agwrite.c -o agwrite.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz -DGRAPHVIZ_2_4_TO_2_9 -I/usr/local/include -fpic -g -O2 -Wall -c bezier.c -o bezier.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz -DGRAPHVIZ_2_4_TO_2_9 -I/usr/local/include -fpic -g -O2 -Wall -c buildEdgeList.c -o buildEdgeList.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz -DGRAPHVIZ_2_4_TO_2_9 -I/usr/local/include -fpic -g -O2 -Wall -c buildNodeList.c -o buildNodeList.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz -DGRAPHVIZ_2_4_TO_2_9 -I/usr/local/include -fpic -g -O2 -Wall -c doLayout.c -o doLayout.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz -DGRAPHVIZ_2_4_TO_2_9 -I/usr/local/include -fpic -g -O2 -Wall -c graphvizVersion.c -o graphvizVersion.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz -DGRAPHVIZ_2_4_TO_2_9 -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz -DGRAPHVIZ_2_4_TO_2_9 -I/usr/local/include -fpic -g -O2 -Wall -c LL_funcs.c -o LL_funcs.o
LL_funcs.c: In function `Rgraphviz_getDefAttrsGraph':
LL_funcs.c:67: warning: unused variable `at_name'
LL_funcs.c:67: warning: unused variable `at_val'
LL_funcs.c: In function `Rgraphviz_toFile':
LL_funcs.c:445: warning: unused variable `i1'
LL_funcs.c:447: warning: unused variable `i2'
LL_funcs.c:449: warning: unused variable `i3'
LL_funcs.c: In function `Rgraphviz_getDefAttrsEdge':
LL_funcs.c:368: warning: `val' might 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_4_TO_2_9 -I/usr/local/include -fpic -g -O2 -Wall -c Rgraphviz.c -o Rgraphviz.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include/graphviz -DGRAPHVIZ_2_4_TO_2_9 -I/usr/local/include -fpic -g -O2 -Wall -c RgraphvizInit.c -o RgraphvizInit.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rgraphviz.so agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o LL_funcs.o Rgraphviz.o RgraphvizInit.o -L/usr/local/lib/graphviz -lgvc
** R
** inst
** save image
Loading required package: graph
Loading required package: geneplotter
Loading required package: annotate
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Creating a new generic function for "lines" in "Rgraphviz"
Creating a new generic function for "plot" in "Rgraphviz"
Warning messages:
1: '\#' is an unrecognized escape in a character string
2: unrecognized escape removed from "\" USEMAP=\#"
** help
>>> Building/Updating help pages for package 'Rgraphviz'
Formats: text html latex example
AgEdge-class text html latex example
AgNode-class text html latex example
AgTextLabel-class text html latex example
BezierCurve-class text html latex example
GraphvizAttributes text html latex example
GraphvizLayouts text html latex example
Ragraph-class text html latex example
agopen text html latex example
agwrite text html latex example
boundingBox-class text html latex example
buildNodeList text html latex example
getAttrs text html latex example
getDefAttrs text html latex example
getDefaultAttrs text html latex example
graphvizVersion text html latex example
imageMap text html latex example
layoutGraph text html latex example
makeNodeAttrs text html latex example
pEdge-class text html latex example
pNode-class text html latex example
pieGlyph text html latex example
plot-methods text html latex example
removedEdges text html latex example
setAttrs text html latex example
toDot-methods text html latex example
toFile text html latex example
xyPoint-class text html latex example
** building package indices ...
* DONE (Rgraphviz)
* creating vignettes ... ERROR
Loading required package: graph
Loading required package: geneplotter
Loading required package: annotate
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: lattice
Loading required package: fibroEset
Loading required package: hgu95av2
Error: chunk 4 (label=plotNeato)
Error in agopen(x, name = name, layout = TRUE, layoutType = y, attrs = attrs, :
There is a bad interaction between Rgraphviz and Graphviz 2.4, 2.6 and 2.8 involving graphs with singleton nodes laid out with neato.
Hopefully we can find a solution, but until then you can use Graphviz versions earlier than 2.4 or newer than 2.8
Error in buildVignettes(dir = ".") : Error: chunk 4 (label=plotNeato)
Error in agopen(x, name = name, layout = TRUE, layoutType = y, attrs = attrs, :
There is a bad interaction between Rgraphviz and Graphviz 2.4, 2.6 and 2.8 involving graphs with singleton nodes laid out with neato.
Hopefully we can find a solution, but until then you can use Graphviz versions earlier than 2.4 or newer than 2.8
Execution halted