BioC 3.1: CHECK report for graph on zin2

Package: graph

Version: 1.46.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.46.0.tar.gz

StartedAt: 2015-10-09 02:12:00 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:13:22 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 81.9 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.46.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/graph.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ version ‘1.46.0’
* 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 ... [3s/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 ... 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 ... [2s/3s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘graph_unit_tests.R’ [13s/17s]
 [13s/17s] 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
  ‘/home/biocbuild/bbs-3.1-bioc/meat/graph.Rcheck/00check.log’
for details.

* installing *source* package ‘graph’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c graph.c -o graph.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o graph.so graph.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
mv graph.so BioC_graph.so
installing to /home/biocbuild/bbs-3.1-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	0.022	0.000	0.027
IMCA	0.176	0.000	0.310
MAPKsig	0.083	0.004	0.147
MultiGraph-class	0.061	0.000	0.061
acc-methods	0.01	0.00	0.01
addEdge	0.006	0.000	0.006
addNode	0.007	0.000	0.007
adj-methods	0.003	0.000	0.003
adjacencyMatrix	0.002	0.000	0.002
apoptosisGraph	0.02	0.00	0.02
attrData-class	0.002	0.000	0.002
aveNumEdges	0.003	0.004	0.007
biocRepos	0.002	0.000	0.002
boundary	0.007	0.000	0.006
calcProb	0	0	0
calcSumProb	0.005	0.000	0.005
clearNode	0.007	0.000	0.007
clusterGraph-class	0.003	0.000	0.007
clusteringCoefficient-methods	0.006	0.000	0.006
combineNodes	0.023	0.000	0.059
distGraph-class	0.001	0.000	0.002
duplicatedEdges	0.001	0.000	0.012
edgeMatrix	0.009	0.000	0.010
edgeSets	0.035	0.000	0.074
edgeWeights	0.005	0.000	0.010
fromGXL-methods	0.250	0.007	0.457
graph-class	0.006	0.004	0.016
graph2SparseM	0.086	0.003	0.187
graphAM-class	0.011	0.000	0.010
graphBAM-class	0.031	0.000	0.031
graphExamples	0.004	0.000	0.004
graphNEL-class	0.004	0.000	0.004
inEdges	0.003	0.000	0.003
leaves	0.008	0.000	0.008
listEdges	0.009	0.000	0.009
matrix2Graph	0.02	0.00	0.02
mostEdges	0.014	0.000	0.014
numNoEdges	0.003	0.000	0.003
pancrCaIni	0.083	0.000	0.083
randomEGraph	0.005	0.000	0.005
randomGraph	0.004	0.000	0.005
randomNodeGraph	0.004	0.000	0.003
removeEdge	0.006	0.000	0.006
removeNode	0.003	0.000	0.002
renderInfo-class	0.006	0.000	0.009
reverseEdgeDirections	0.005	0.000	0.005
simpleEdge-class	0.004	0.000	0.004
standardLabeling	0.062	0.000	0.062
subGraph	0.001	0.000	0.001
toDotR-methods	0.021	0.000	0.021
ugraph	0.005	0.000	0.005
validGraph	0.001	0.000	0.001