BioC 3.2: CHECK report for graph on zin1

Package: graph

Version: 1.48.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.48.0.tar.gz

StartedAt: 2016-04-23 01:34:48 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:35:43 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 54.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: graph.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.48.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/graph.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.48.0’
* 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 ... [3s/3s] 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 ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘graph_unit_tests.R’ [13s/13s]
 [13s/13s] 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/graph.Rcheck/00check.log’
for details.

* installing *source* package ‘graph’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-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-3.2-bioc/R/lib -L/usr/local/lib -o graph.so graph.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
mv graph.so BioC_graph.so
installing to /home/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	0.022	0.000	0.021
IMCA	0.168	0.003	0.172
MAPKsig	0.076	0.008	0.084
MultiGraph-class	0.062	0.004	0.066
acc-methods	0.009	0.000	0.009
addEdge	0.006	0.000	0.006
addNode	0.006	0.000	0.007
adj-methods	0.004	0.000	0.003
adjacencyMatrix	0.003	0.000	0.002
apoptosisGraph	0.02	0.00	0.02
attrData-class	0.002	0.000	0.002
aveNumEdges	0.008	0.000	0.008
biocRepos	0.002	0.000	0.002
boundary	0.005	0.000	0.005
calcProb	0.000	0.000	0.001
calcSumProb	0.006	0.000	0.006
clearNode	0.008	0.000	0.008
clusterGraph-class	0.003	0.000	0.003
clusteringCoefficient-methods	0.007	0.000	0.007
combineNodes	0.023	0.000	0.023
distGraph-class	0.001	0.000	0.001
duplicatedEdges	0	0	0
edgeMatrix	0.009	0.000	0.009
edgeSets	0.033	0.000	0.033
edgeWeights	0.006	0.000	0.006
fromGXL-methods	0.233	0.008	0.241
graph-class	0.006	0.000	0.006
graph2SparseM	0.085	0.000	0.086
graphAM-class	0.007	0.000	0.008
graphBAM-class	0.03	0.00	0.03
graphExamples	0.004	0.000	0.004
graphNEL-class	0.003	0.000	0.003
inEdges	0.002	0.000	0.002
leaves	0.006	0.004	0.010
listEdges	0.007	0.000	0.008
matrix2Graph	0.019	0.000	0.018
mostEdges	0.014	0.000	0.014
numNoEdges	0.003	0.000	0.003
pancrCaIni	0.078	0.004	0.083
randomEGraph	0.002	0.004	0.005
randomGraph	0.004	0.000	0.005
randomNodeGraph	0.003	0.000	0.003
removeEdge	0.006	0.000	0.005
removeNode	0.002	0.000	0.003
renderInfo-class	0.009	0.000	0.008
reverseEdgeDirections	0.005	0.000	0.004
simpleEdge-class	0.001	0.000	0.001
standardLabeling	0.054	0.004	0.059
subGraph	0.002	0.000	0.002
toDotR-methods	0.019	0.000	0.019
ugraph	0.006	0.000	0.005
validGraph	0.012	0.000	0.013