BioC 3.3: CHECK report for graph on morelia

Package: graph

Version: 1.49.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings graph_1.49.1.tar.gz

StartedAt: 2016-04-21 03:32:05 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 03:33:32 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 87.6 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

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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_1.49.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/graph.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.49.1’
* 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 ... [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
.mg_validate_node_names: no visible global function definition for
  ‘head’
MultiDiGraph: no visible global function definition for ‘head’
plot,graph-ANY: no visible global function definition for ‘getMethod’
show,MultiGraph: no visible global function definition for ‘head’
Undefined global functions or variables:
  getMethod head
Consider adding
  importFrom("methods", "getMethod")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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’ [17s/18s]
 [18s/18s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-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-3.3-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	0.031	0.003	0.034
IMCA	0.191	0.006	0.197
MAPKsig	0.181	0.007	0.190
MultiGraph-class	0.106	0.004	0.109
acc-methods	0.018	0.001	0.017
addEdge	0.01	0.00	0.01
addNode	0.010	0.001	0.010
adj-methods	0.005	0.000	0.005
adjacencyMatrix	0.005	0.001	0.009
apoptosisGraph	0.023	0.001	0.026
attrData-class	0.003	0.001	0.003
aveNumEdges	0.011	0.001	0.013
biocRepos	0.003	0.001	0.007
boundary	0.011	0.000	0.015
calcProb	0.000	0.000	0.001
calcSumProb	0.008	0.000	0.008
clearNode	0.012	0.001	0.014
clusterGraph-class	0.004	0.000	0.005
clusteringCoefficient-methods	0.009	0.001	0.010
combineNodes	0.034	0.000	0.040
distGraph-class	0.002	0.001	0.002
duplicatedEdges	0.000	0.000	0.003
edgeMatrix	0.016	0.001	0.018
edgeSets	0.049	0.018	0.077
edgeWeights	0.009	0.001	0.015
fromGXL-methods	0.364	0.008	0.382
graph-class	0.010	0.001	0.010
graph2SparseM	0.133	0.006	0.138
graphAM-class	0.032	0.001	0.032
graphBAM-class	0.048	0.001	0.050
graphExamples	0.007	0.001	0.007
graphNEL-class	0.007	0.000	0.007
inEdges	0.004	0.000	0.004
leaves	0.015	0.002	0.017
listEdges	0.012	0.000	0.013
matrix2Graph	0.031	0.001	0.033
mostEdges	0.018	0.000	0.019
numNoEdges	0.005	0.000	0.004
pancrCaIni	0.111	0.002	0.114
randomEGraph	0.008	0.000	0.010
randomGraph	0.011	0.000	0.012
randomNodeGraph	0.005	0.000	0.006
removeEdge	0.009	0.000	0.010
removeNode	0.004	0.000	0.005
renderInfo-class	0.012	0.000	0.012
reverseEdgeDirections	0.007	0.000	0.007
simpleEdge-class	0.002	0.000	0.002
standardLabeling	0.065	0.002	0.067
subGraph	0.003	0.000	0.003
toDotR-methods	0.034	0.012	0.046
ugraph	0.010	0.000	0.015
validGraph	0.003	0.000	0.007