BioC 2.9: CHECK report for Rgraphviz on liverpool

Package: Rgraphviz

Version: 1.31.1

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch Rgraphviz_1.31.1.tar.gz

StartedAt: 2011-07-07 03:22:29 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 03:23:18 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 49.6 seconds

RetCode: 0

Status: OK

CheckDir: Rgraphviz.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/Rgraphviz.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rgraphviz/DESCRIPTION' ... OK
* this is package 'Rgraphviz' version '1.31.1'
* 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 installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* 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) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'Rgraphviz' ...
Using the following environment variables
GRAPHVIZ_INSTALL_DIR=C:\/Graphviz2.20
GRAPHVIZ_INSTALL_MAJOR=2
GRAPHVIZ_INSTALL_MINOR=20
GRAPHVIZ_INSTALL_SUBMINOR=3
Using the following compilation and linking flags for Rgraphviz
   PKG_CPPFLAGS=-IC:\/Graphviz2.20/include/graphviz
   PKG_LIBS=-LC:\/Graphviz2.20/bin -lgvc-4 -lgraph-4 -lcdt-4
   GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32
Created file src/Makevars.win
Created file R/graphviz_build_version.R
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -IC:/Graphviz2.20/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32         -O3 -Wall  -std=gnu99 -c LL_funcs.c -o LL_funcs.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -IC:/Graphviz2.20/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32         -O3 -Wall  -std=gnu99 -c Rgraphviz.c -o Rgraphviz.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -IC:/Graphviz2.20/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32         -O3 -Wall  -std=gnu99 -c RgraphvizInit.c -o RgraphvizInit.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -IC:/Graphviz2.20/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32         -O3 -Wall  -std=gnu99 -c agopen.c -o agopen.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -IC:/Graphviz2.20/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32         -O3 -Wall  -std=gnu99 -c agread.c -o agread.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -IC:/Graphviz2.20/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32         -O3 -Wall  -std=gnu99 -c agwrite.c -o agwrite.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -IC:/Graphviz2.20/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32         -O3 -Wall  -std=gnu99 -c bezier.c -o bezier.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -IC:/Graphviz2.20/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32         -O3 -Wall  -std=gnu99 -c buildEdgeList.c -o buildEdgeList.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -IC:/Graphviz2.20/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32         -O3 -Wall  -std=gnu99 -c buildNodeList.c -o buildNodeList.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -IC:/Graphviz2.20/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32         -O3 -Wall  -std=gnu99 -c doLayout.c -o doLayout.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -IC:/Graphviz2.20/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32         -O3 -Wall  -std=gnu99 -c graphvizVersion.c -o graphvizVersion.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -IC:/Graphviz2.20/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32         -O3 -Wall  -std=gnu99 -c init.c -o init.o
gcc -shared -s -static-libgcc -o Rgraphviz.dll tmp.def LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o -LC:/Graphviz2.20/bin -lgvc-4 -lgraph-4 -lcdt-4 -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/Rgraphviz.Rcheck/Rgraphviz/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for "head" from package "utils" in package "Rgraphviz"
Creating a generic function for "tail" from package "utils" in package "Rgraphviz"
Creating a generic function for "lines" from package "graphics" in package "Rgraphviz"
Creating a generic function for "plot" from package "graphics" in package "Rgraphviz"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'Rgraphviz.Rnw' 
   'newRgraphvizInterface.Rnw' 
** testing if installed package can be loaded

* DONE (Rgraphviz)

name	user	system	elapsed
AgEdge-class	0.09	0.00	0.09
AgNode-class	0.02	0.00	0.02
AgTextLabel-class	0.01	0.00	0.02
BezierCurve-class	0.02	0.00	0.01
GraphvizLayouts	0.01	0.00	0.02
Ragraph-class	0.05	0.00	0.04
agopen	0.03	0.00	0.05
agopenSimple	0.05	0.00	0.05
agwrite	0.01	0.00	0.01
boundingBox-class	0.02	0.00	0.02
buildNodeList	0	0	0
clusterData-methods	0.45	0.03	0.61
getDefaultAttrs	0.02	0.00	0.01
graphLayout	0	0	0
graphvizVersion	0	0	0
layoutGraph	0.25	0.00	0.25
makeNodeAttrs	0	0	0
pEdge-class	0.02	0.00	0.01
pNode-class	0	0	0
pieGlyph	0.01	0.00	0.02
plot-methods	0	0	0
removedEdges	0	0	0
renderGraph	0.2	0.0	0.2
toDot-methods	0.02	0.00	0.03
toFile	0.08	0.01	0.23
xyPoint-class	0	0	0

Summary

Command output