BioC 3.2: CHECK report for graph on oaxaca

Package: graph

Version: 1.48.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings graph_1.48.0.tar.gz

StartedAt: 2016-04-23 00:53:49 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:55:12 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 83.3 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_1.48.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/graph.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ version ‘1.48.0’
* 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 ... [5s/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/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘graph_unit_tests.R’ [15s/16s]
 [16s/16s] 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
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c graph.c -o graph.o
clang -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 -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	0.030	0.001	0.030
IMCA	0.177	0.005	0.373
MAPKsig	0.106	0.006	0.505
MultiGraph-class	0.090	0.003	0.111
acc-methods	0.011	0.000	0.012
addEdge	0.011	0.000	0.012
addNode	0.005	0.000	0.012
adj-methods	0.003	0.000	0.003
adjacencyMatrix	0.004	0.000	0.004
apoptosisGraph	0.031	0.002	0.033
attrData-class	0.003	0.000	0.043
aveNumEdges	0.009	0.001	0.010
biocRepos	0.002	0.000	0.003
boundary	0.006	0.000	0.007
calcProb	0.001	0.000	0.001
calcSumProb	0.006	0.000	0.006
clearNode	0.010	0.000	0.009
clusterGraph-class	0.004	0.000	0.004
clusteringCoefficient-methods	0.008	0.001	0.008
combineNodes	0.031	0.000	0.031
distGraph-class	0.005	0.001	0.004
duplicatedEdges	0.001	0.000	0.000
edgeMatrix	0.013	0.001	0.013
edgeSets	0.045	0.014	0.060
edgeWeights	0.008	0.001	0.010
fromGXL-methods	0.362	0.010	0.373
graph-class	0.008	0.001	0.009
graph2SparseM	0.123	0.003	0.126
graphAM-class	0.015	0.000	0.015
graphBAM-class	0.039	0.000	0.039
graphExamples	0.005	0.001	0.006
graphNEL-class	0.003	0.000	0.004
inEdges	0.003	0.000	0.004
leaves	0.013	0.002	0.014
listEdges	0.012	0.000	0.012
matrix2Graph	0.022	0.001	0.023
mostEdges	0.019	0.001	0.020
numNoEdges	0.005	0.000	0.005
pancrCaIni	0.116	0.002	0.254
randomEGraph	0.005	0.000	0.005
randomGraph	0.005	0.000	0.005
randomNodeGraph	0.005	0.001	0.005
removeEdge	0.007	0.000	0.007
removeNode	0.004	0.000	0.004
renderInfo-class	0.008	0.001	0.008
reverseEdgeDirections	0.006	0.000	0.007
simpleEdge-class	0.003	0.001	0.003
standardLabeling	0.063	0.002	0.065
subGraph	0.003	0.000	0.003
toDotR-methods	0.032	0.003	0.035
ugraph	0.008	0.001	0.008
validGraph	0.003	0.000	0.002