BioC 2.13: CHECK report for graph on perceval

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/graph.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ version ‘1.40.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graph’ can be installed ... [8s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘clusterGraph.Rnw’, ‘graph.Rnw’, ‘graphAttributes.Rnw’,
  ‘GraphClass.Rnw’, ‘MultiGraphClass.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [6s/6s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘graph_unit_tests.R’ [32s/32s]
 [32s/33s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/graph.Rcheck/00check.log’
for details.

* installing *source* package ‘graph’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c graph.c -o graph.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o graph.so graph.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
mv graph.so BioC_graph.so
installing to /Users/biocbuild/bbs-2.13-bioc/meat/graph.Rcheck/graph/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (graph)

name	user	system	elapsed
DFS	0.056	0.003	0.060
IMCA	0.312	0.015	0.331
MAPKsig	0.181	0.009	0.192
MultiGraph-class	0.160	0.005	0.168
acc-methods	0.032	0.001	0.033
addEdge	0.032	0.000	0.033
addNode	0.031	0.001	0.033
adj-methods	0.018	0.001	0.019
apoptosisGraph	0.088	0.005	0.094
attrData-class	0.022	0.001	0.023
aveNumEdges	0.021	0.000	0.022
biocRepos	0.006	0.000	0.007
boundary	0.015	0.000	0.016
calcProb	0.003	0.000	0.004
calcSumProb	0.018	0.001	0.020
clearNode	0.020	0.001	0.022
clusterGraph-class	0.013	0.000	0.014
clusteringCoefficient-methods	0.023	0.001	0.024
combineNodes	0.062	0.002	0.063
distGraph-class	0.016	0.001	0.016
duplicatedEdges	0.006	0.000	0.007
edgeMatrix	0.051	0.003	0.054
edgeSets	0.047	0.005	0.053
edgeWeights	0.024	0.001	0.025
fromGXL-methods	0.417	0.020	0.437
graph-class	0.145	0.002	0.148
graph2SparseM	0.199	0.013	0.213
graphAM-class	0.031	0.001	0.033
graphBAM-class	0.115	0.004	0.120
graphExamples	0.022	0.001	0.023
graphNEL-class	0.038	0.002	0.039
inEdges	0.029	0.001	0.029
leaves	0.030	0.002	0.031
listEdges	0.197	0.003	0.201
matrix2Graph	0.090	0.002	0.098
mostEdges	0.046	0.001	0.047
numNoEdges	0.028	0.001	0.028
pancrCaIni	0.199	0.011	0.212
randomEGraph	0.031	0.000	0.032
randomGraph	0.030	0.001	0.031
randomNodeGraph	0.025	0.001	0.025
removeEdge	0.042	0.001	0.043
removeNode	0.027	0.001	0.028
renderInfo-class	0.051	0.002	0.053
reverseEdgeDirections	0.042	0.001	0.044
simpleEdge-class	0.020	0.001	0.021
standardLabeling	0.077	0.005	0.084
subGraph	0.020	0.002	0.023
toDotR-methods	0.059	0.004	0.064
ugraph	0.027	0.001	0.028
validGraph	0.030	0.000	0.031

BioC 2.13: CHECK report for graph on perceval

Summary

Command output