Multiple platform build/check report for BioC 3.10 - CHECK report for graph on merida1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:graph.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings graph_1.64.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/graph.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.64.0’
* 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'edgeMatrix':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/graph.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL graph
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘graph’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-graph/00new/graph/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (graph)

Tests output


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min



RUNIT TEST PROTOCOL -- Wed Apr 15 02:53:56 2020 
*********************************************** 
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 
> 
> proc.time()
   user  system elapsed 
  6.182   0.172   6.483

Example timings

name	user	system	elapsed
DFS	0.044	0.005	0.049
IMCA	0.143	0.024	0.168
MAPKsig	0.151	0.004	0.156
MultiGraph-class	0.229	0.004	0.234
acc-methods	0.010	0.001	0.011
addEdge	0.07	0.00	0.07
addNode	0.012	0.000	0.013
adj-methods	0.003	0.000	0.003
adjacencyMatrix	0.004	0.000	0.003
apoptosisGraph	0.021	0.002	0.023
attrData-class	0.002	0.000	0.002
aveNumEdges	0.006	0.001	0.006
biocRepos	0.001	0.000	0.002
boundary	0.003	0.000	0.003
calcProb	0.000	0.000	0.001
calcSumProb	0.005	0.000	0.005
clearNode	0.019	0.000	0.020
clusterGraph-class	0.014	0.000	0.015
clusteringCoefficient-methods	0.048	0.001	0.049
combineNodes	0.099	0.001	0.100
distGraph-class	0.002	0.000	0.001
duplicatedEdges	0	0	0
edgeMatrix	0.012	0.001	0.014
edgeSets	0.041	0.009	0.050
edgeWeights	0.012	0.000	0.013
fromGXL-methods	0.238	0.008	0.248
graph-class	0.006	0.001	0.007
graph2SparseM	0.111	0.003	0.113
graphAM-class	0.008	0.000	0.010
graphBAM-class	0.048	0.002	0.050
graphExamples	0.006	0.001	0.009
graphNEL-class	0.009	0.001	0.009
inEdges	0.008	0.000	0.008
leaves	0.012	0.002	0.015
listEdges	0.012	0.001	0.014
matrix2Graph	0.026	0.001	0.027
mostEdges	0.005	0.000	0.006
numNoEdges	0.003	0.000	0.003
pancrCaIni	0.220	0.003	0.238
randomEGraph	0.007	0.000	0.007
randomGraph	0.003	0.000	0.003
randomNodeGraph	0.002	0.000	0.003
removeEdge	0.011	0.000	0.011
removeNode	0.006	0.000	0.006
renderInfo-class	0.006	0.000	0.007
reverseEdgeDirections	0.004	0.001	0.004
simpleEdge-class	0.001	0.000	0.002
standardLabeling	0.067	0.002	0.068
subGraph	0.002	0.001	0.002
toDotR-methods	0.023	0.003	0.026
ugraph	0.012	0.000	0.013
validGraph	0.001	0.000	0.001

CHECK report for graph on merida1

Summary

Command output

Installation output

Tests output

Example timings