Package: graph

Version: 1.56.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings graph_1.56.0.tar.gz

StartedAt: 2018-04-12 04:45:08 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 04:46:26 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 77.5 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_1.56.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/graph.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ version ‘1.56.0’
* 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 ... 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 ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-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   -fPIC  -Wall -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-3.6-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)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("graph", pattern="_test.R")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min



RUNIT TEST PROTOCOL -- Thu Apr 12 04:46:19 2018 
*********************************************** 
Number of test functions: 206 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
graph RUnit Tests - 206 test functions, 0 errors, 0 failures
Number of test functions: 206 
Number of errors: 0 
Number of failures: 0 
Warning message:
In readLines(con) : seek on a gzfile connection returned an internal error
> 
> proc.time()
   user  system elapsed 
 18.888   0.141  19.339 

name	user	system	elapsed
DFS	0.072	0.004	0.076
IMCA	0.130	0.006	0.140
MAPKsig	0.385	0.008	0.412
MultiGraph-class	0.646	0.005	0.673
acc-methods	0.100	0.001	0.103
addEdge	0.046	0.000	0.048
addNode	0.023	0.001	0.026
adj-methods	0.003	0.000	0.004
adjacencyMatrix	0.003	0.001	0.004
apoptosisGraph	0.019	0.002	0.020
attrData-class	0.003	0.001	0.004
aveNumEdges	0.009	0.000	0.010
biocRepos	0.002	0.001	0.004
boundary	0.004	0.000	0.004
calcProb	0	0	0
calcSumProb	0.078	0.000	0.078
clearNode	0.011	0.000	0.011
clusterGraph-class	0.01	0.00	0.01
clusteringCoefficient-methods	0.039	0.000	0.042
combineNodes	0.128	0.001	0.131
distGraph-class	0.002	0.000	0.003
duplicatedEdges	0.001	0.000	0.001
edgeMatrix	0.044	0.000	0.045
edgeSets	0.043	0.007	0.050
edgeWeights	0.014	0.001	0.014
fromGXL-methods	0.482	0.011	0.498
graph-class	0.006	0.001	0.006
graph2SparseM	0.095	0.003	0.097
graphAM-class	0.039	0.001	0.039
graphBAM-class	0.262	0.002	0.268
graphExamples	0.003	0.000	0.003
graphNEL-class	0.009	0.000	0.009
inEdges	0.007	0.001	0.007
leaves	0.010	0.002	0.012
listEdges	0.009	0.001	0.010
matrix2Graph	0.036	0.001	0.037
mostEdges	0.005	0.000	0.004
numNoEdges	0.002	0.000	0.002
pancrCaIni	0.183	0.003	0.187
randomEGraph	0.005	0.000	0.006
randomGraph	0.005	0.000	0.005
randomNodeGraph	0.003	0.000	0.007
removeEdge	0.045	0.001	0.046
removeNode	0.007	0.000	0.008
renderInfo-class	0.061	0.001	0.062
reverseEdgeDirections	0.005	0.001	0.005
simpleEdge-class	0.001	0.000	0.001
standardLabeling	0.050	0.002	0.053
subGraph	0.002	0.000	0.002
toDotR-methods	0.041	0.002	0.042
ugraph	0.010	0.000	0.011
validGraph	0.002	0.000	0.002