Package: graph

Version: 1.31.1

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch graph_1.31.1.tar.gz

StartedAt: 2011-07-07 02:12:57 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 02:14:13 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 75.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: graph.Rcheck

Warnings: 1

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/graph.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 'graph/DESCRIPTION' ... OK
* this is package 'graph' version '1.31.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory 'src' contains:
  BioC_graph.dll
These are unlikely file names for src files.
* checking whether package 'graph' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 tests ... OK
* checking tests ...
  Running 'graph_unit_tests.R'
 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

WARNING: There was 1 warning, see
  'E:/biocbld/bbs-2.9-bioc/meat/graph.Rcheck/00check.log'
for details

* installing *source* package 'graph' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c graph.c -o graph.o
gcc -shared -s -static-libgcc -o graph.dll tmp.def graph.o -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
mv graph.dll BioC_graph.dll
installing to E:/biocbld/bbs-2.9-bioc/meat/graph.Rcheck/graph/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'GraphClass.Rnw' 
   'MultiGraphClass.Rnw' 
   'clusterGraph.Rnw' 
   'graph.Rnw' 
   'graphAttributes.Rnw' 
** testing if installed package can be loaded

* DONE (graph)

name	user	system	elapsed
DFS	0.06	0.00	0.06
IMCA	0.20	0.02	0.23
MAPKsig	0.14	0.00	0.46
MultiGraph-class	0.11	0.00	0.11
acc-methods	0.02	0.00	0.01
addEdge	0.01	0.00	0.02
addNode	0.02	0.00	0.01
adj-methods	0.01	0.00	0.02
apoptosisGraph	0.04	0.00	0.03
attrData-class	0	0	0
aveNumEdges	0.01	0.00	0.02
biocRepos	0	0	0
boundary	0.02	0.00	0.01
buildRepDepGraph	0	0	0
calcProb	0	0	0
calcSumProb	0.01	0.00	0.02
clearNode	0.00	0.00	0.01
clusterGraph-class	0	0	0
clusteringCoefficient-methods	0.02	0.00	0.02
combineNodes	0.06	0.00	0.06
distGraph-class	0	0	0
duplicatedEdges	0	0	0
edgeMatrix	0.02	0.00	0.02
edgeSets	0.04	0.00	0.04
edgeWeights	0.03	0.00	0.03
fromGXL-methods	0.50	0.01	0.54
graph-class	0.02	0.00	0.01
graph2SparseM	0.23	0.00	0.24
graphAM-class	0	0	0
graphBAM-class	0.07	0.00	0.06
graphExamples	0.01	0.00	0.02
graphNEL-class	0	0	0
inEdges	0.02	0.00	0.01
leaves	0.01	0.00	0.02
listEdges	0.02	0.00	0.02
matrix2Graph	0.03	0.00	0.03
mostEdges	0.02	0.00	0.01
numNoEdges	0	0	0
pancrCaIni	0.10	0.00	0.09
randomEGraph	0.01	0.00	0.02
randomGraph	0	0	0
randomNodeGraph	0.02	0.00	0.01
removeEdge	0.01	0.00	0.02
removeNode	0	0	0
renderInfo-class	0.02	0.00	0.01
reverseEdgeDirections	0.01	0.00	0.02
simpleEdge-class	0	0	0
standardLabeling	0.11	0.00	0.11
subGraph	0	0	0
toDotR-methods	0.03	0.00	0.36
ugraph	0.02	0.00	0.01
validGraph	0.06	0.00	0.07