BioC 3.2: CHECK report for graph on perceval

Package: graph

Version: 1.47.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings graph_1.47.2.tar.gz

StartedAt: 2015-08-24 01:31:44 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:33:14 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 90.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: graph.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings graph_1.47.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/graph.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.47.2’
* 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 ... [6s/6s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
'library' or 'require' call to ‘package’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gxlTreeNEL: no visible global function definition for ‘xmlOutputDOM’
combineNodes,character-graphNEL-character : .local: no visible binding
  for global variable ‘from’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  ‘dist’
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 GNU extensions in Makefiles ... 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 files in ‘vignettes’ ... OK
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘graph_unit_tests.R’ [24s/24s]
 [25s/25s] 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
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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/Library/Frameworks/R.framework/Resources/lib -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-3.2-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	0.033	0.001	0.034
IMCA	0.329	0.005	0.334
MAPKsig	0.144	0.013	0.190
MultiGraph-class	0.083	0.003	0.088
acc-methods	0.013	0.001	0.014
addEdge	0.009	0.000	0.009
addNode	0.009	0.000	0.010
adj-methods	0.005	0.001	0.005
adjacencyMatrix	0.005	0.000	0.005
apoptosisGraph	0.062	0.001	0.063
attrData-class	0.003	0.000	0.003
aveNumEdges	0.014	0.000	0.014
biocRepos	0.003	0.001	0.003
boundary	0.007	0.000	0.007
calcProb	0.001	0.000	0.001
calcSumProb	0.007	0.000	0.007
clearNode	0.011	0.001	0.011
clusterGraph-class	0.004	0.000	0.004
clusteringCoefficient-methods	0.008	0.000	0.009
combineNodes	0.034	0.001	0.035
distGraph-class	0.002	0.000	0.002
duplicatedEdges	0.000	0.000	0.001
edgeMatrix	0.014	0.001	0.015
edgeSets	0.041	0.021	0.063
edgeWeights	0.008	0.000	0.007
fromGXL-methods	0.422	0.016	0.438
graph-class	0.009	0.001	0.009
graph2SparseM	0.136	0.004	0.140
graphAM-class	0.010	0.001	0.010
graphBAM-class	0.048	0.001	0.049
graphExamples	0.006	0.000	0.006
graphNEL-class	0.005	0.000	0.004
inEdges	0.003	0.000	0.003
leaves	0.010	0.000	0.011
listEdges	0.01	0.00	0.01
matrix2Graph	0.028	0.001	0.029
mostEdges	0.018	0.001	0.020
numNoEdges	0.004	0.000	0.004
pancrCaIni	0.149	0.005	0.153
randomEGraph	0.006	0.000	0.006
randomGraph	0.006	0.001	0.006
randomNodeGraph	0.004	0.000	0.005
removeEdge	0.007	0.001	0.008
removeNode	0.003	0.000	0.004
renderInfo-class	0.008	0.001	0.009
reverseEdgeDirections	0.005	0.000	0.005
simpleEdge-class	0.001	0.000	0.001
standardLabeling	0.060	0.003	0.062
subGraph	0.002	0.000	0.002
toDotR-methods	0.186	0.004	0.189
ugraph	0.007	0.001	0.007
validGraph	0.002	0.000	0.002