Rgraphviz 1.17.11
Li Long
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rgraphviz | | Last Changed Rev: 29139 / Revision: 29143 | | Last Changed Date: 2007-12-10 19:00:09 -0800 (Mon, 10 Dec 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | WARNINGS | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | WARNINGS | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | [ WARNINGS ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | ERROR | skipped | skipped |
| lemming | Windows Server 2003 (32-bit) / x64 | ERROR | skipped | skipped |
* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/Rgraphviz.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-09 r43632)
* checking for file 'Rgraphviz/DESCRIPTION' ... OK
* this is package 'Rgraphviz' version '1.17.11'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Rgraphviz' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'renderGraph':
"\\S4method{renderGraph}{graph}"{x, drawNodes, drawEdges,graph.pars}
Functions with \usage entries need to have the appropriate \alias entries,
and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating Rgraphviz-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... NOTE
--- running texi2dvi on vignettes
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './Rgraphviz.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './Rgraphviz.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './Rgraphviz.tex' ...
* creating Rgraphviz-manual.tex ... OK
* checking Rgraphviz-manual.tex ... OK
WARNING: There was 1 warning, see
/loc/home/biocbuild/bbs-2.2-bioc/meat/Rgraphviz.Rcheck/00check.log
for details
/loc/home/biocbuild/bbs-2.2-bioc/meat/Rgraphviz.Rcheck
* Installing *source* package 'Rgraphviz' ...
configure: No --with-graphviz option was specified. Trying to find graphviz using other methods.
checking for pkg-config... /usr/bin/pkg-config
configure: Found graphviz 2.14.1
configure: We have inferred the following flags for graphviz
configure: ..PKG_CPPFLAGS=-I/usr/include/graphviz
configure: ..PKG_LIBS=-lgvc
checking for whether compiler has bool... checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=14 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include -fpic -g -O2 -Wall -c agopen.c -o agopen.o
In file included from /usr/include/graphviz/gvc.h:20,
from common.h:31,
from agopen.c:1:
/usr/include/graphviz/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
from agopen.c:1:
/home/biocbuild/bbs-2.2-bioc/R/include/Rdefines.h:149:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=14 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include -fpic -g -O2 -Wall -c agread.c -o agread.o
In file included from /usr/include/graphviz/gvc.h:20,
from common.h:31,
from agread.c:1:
/usr/include/graphviz/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
from agread.c:1:
/home/biocbuild/bbs-2.2-bioc/R/include/Rdefines.h:149:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=14 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include -fpic -g -O2 -Wall -c agwrite.c -o agwrite.o
In file included from /usr/include/graphviz/gvc.h:20,
from common.h:31,
from agwrite.c:1:
/usr/include/graphviz/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
from agwrite.c:1:
/home/biocbuild/bbs-2.2-bioc/R/include/Rdefines.h:149:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=14 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include -fpic -g -O2 -Wall -c bezier.c -o bezier.o
In file included from /usr/include/graphviz/gvc.h:20,
from common.h:31,
from bezier.c:1:
/usr/include/graphviz/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
from bezier.c:1:
/home/biocbuild/bbs-2.2-bioc/R/include/Rdefines.h:149:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=14 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include -fpic -g -O2 -Wall -c buildEdgeList.c -o buildEdgeList.o
In file included from /usr/include/graphviz/gvc.h:20,
from common.h:31,
from buildEdgeList.c:1:
/usr/include/graphviz/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
from buildEdgeList.c:1:
/home/biocbuild/bbs-2.2-bioc/R/include/Rdefines.h:149:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=14 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include -fpic -g -O2 -Wall -c buildNodeList.c -o buildNodeList.o
In file included from /usr/include/graphviz/gvc.h:20,
from common.h:31,
from buildNodeList.c:1:
/usr/include/graphviz/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
from buildNodeList.c:1:
/home/biocbuild/bbs-2.2-bioc/R/include/Rdefines.h:149:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=14 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include -fpic -g -O2 -Wall -c doLayout.c -o doLayout.o
In file included from /usr/include/graphviz/gvc.h:20,
from common.h:31,
from doLayout.c:1:
/usr/include/graphviz/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
from doLayout.c:1:
/home/biocbuild/bbs-2.2-bioc/R/include/Rdefines.h:149:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=14 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include -fpic -g -O2 -Wall -c graphvizVersion.c -o graphvizVersion.o
In file included from /usr/include/graphviz/gvc.h:20,
from common.h:31,
from graphvizVersion.c:1:
/usr/include/graphviz/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
from graphvizVersion.c:1:
/home/biocbuild/bbs-2.2-bioc/R/include/Rdefines.h:149:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=14 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
In file included from /usr/include/graphviz/gvc.h:20,
from common.h:31,
from init.c:1:
/usr/include/graphviz/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
from init.c:1:
/home/biocbuild/bbs-2.2-bioc/R/include/Rdefines.h:149:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=14 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include -fpic -g -O2 -Wall -c LL_funcs.c -o LL_funcs.o
In file included from /usr/include/graphviz/gvc.h:20,
from common.h:31,
from LL_funcs.c:1:
/usr/include/graphviz/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
from LL_funcs.c:1:
/home/biocbuild/bbs-2.2-bioc/R/include/Rdefines.h:149:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=14 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include -fpic -g -O2 -Wall -c Rgraphviz.c -o Rgraphviz.o
In file included from /usr/include/graphviz/gvc.h:20,
from common.h:31,
from Rgraphviz.c:1:
/usr/include/graphviz/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
from Rgraphviz.c:1:
/home/biocbuild/bbs-2.2-bioc/R/include/Rdefines.h:149:1: warning: this is the location of the previous definition
Rgraphviz.c:18: warning: C99 inline functions are not supported; using GNU89
Rgraphviz.c:18: warning: to disable this warning use -fgnu89-inline or the gnu_inline function attribute
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=14 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include -fpic -g -O2 -Wall -c RgraphvizInit.c -o RgraphvizInit.o
In file included from /usr/include/graphviz/gvc.h:20,
from common.h:31,
from RgraphvizInit.c:1:
/usr/include/graphviz/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
from RgraphvizInit.c:1:
/home/biocbuild/bbs-2.2-bioc/R/include/Rdefines.h:149:1: warning: this is the location of the previous definition
gcc -std=gnu99 -shared -L/usr/local/lib -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 -lgvc -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
Loading required package: graph
Loading required package: grid
Creating a new generic function for "head" in "Rgraphviz"
Creating a new generic function for "tail" in "Rgraphviz"
Creating a new generic function for "lines" in "Rgraphviz"
Creating a new generic function for "plot" in "Rgraphviz"
** help
Note: removing empty section \examples
Note: removing empty section \seealso
Note: removing empty section \seealso
Note: removing empty section \seealso
Note: removing empty section \seealso
>>> 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
GraphvizLayouts text html latex example
Ragraph-class text html latex example
agopen text html latex example
agopenSimple text html latex example
agwrite text html latex example
boundingBox-class text html latex example
buildNodeList text html latex example
clusterData-methods text html latex example
getDefaultAttrs text html latex example
graphData-methods text html latex
graphDataDefaults-methods text html latex
graphLayout text html latex example
graphvizVersion 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
renderGraph 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)