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CHECK report for graph on malbec2

This page was generated on 2020-10-17 11:54:54 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE graph PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 771/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graph 1.66.0
Bioconductor Package Maintainer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/graph
Branch: RELEASE_3_11
Last Commit: a09c8a9
Last Changed Date: 2020-04-27 14:08:14 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: graph
Version: 1.66.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:graph.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings graph_1.66.0.tar.gz
StartedAt: 2020-10-17 01:59:13 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:00:17 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 63.9 seconds
RetCode: 0
Status:  OK 
CheckDir: graph.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:graph.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings graph_1.66.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/graph.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.66.0’
* 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 ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/graph.Rcheck/00check.log’
for details.



Installation output

graph.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL graph
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘graph’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c graph.c -o graph.o
gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o graph.so graph.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
mv graph.so BioC_graph.so
installing to /home/biocbuild/bbs-3.11-bioc/R/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

graph.Rcheck/tests/graph_unit_tests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 -- Sat Oct 17 02:00:11 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 
  5.819   0.104   6.805 

Example timings

graph.Rcheck/graph-Ex.timings

nameusersystemelapsed
DFS0.0540.0040.058
IMCA0.2410.0080.259
MAPKsig0.1170.0030.121
MultiGraph-class0.1490.0000.149
acc-methods0.0070.0000.007
addEdge0.0420.0000.042
addNode0.0080.0000.008
adj-methods0.0020.0000.002
adjacencyMatrix0.0020.0000.002
apoptosisGraph0.0140.0000.014
attrData-class0.0010.0000.001
aveNumEdges0.0040.0000.004
biocRepos0.0020.0000.002
boundary0.0070.0000.007
calcProb000
calcSumProb0.0040.0000.004
clearNode0.0110.0000.011
clusterGraph-class0.0080.0000.008
clusteringCoefficient-methods0.0280.0000.028
combineNodes0.0740.0000.074
distGraph-class0.0010.0000.000
duplicatedEdges000
edgeMatrix0.0050.0030.008
edgeSets0.0340.0000.034
edgeWeights0.0080.0010.008
fromGXL-methods0.3010.0000.322
graph-class0.0050.0000.006
graph2SparseM0.1440.0030.146
graphAM-class0.0130.0000.013
graphBAM-class0.0410.0000.040
graphExamples0.0060.0000.006
graphNEL-class0.0090.0000.009
inEdges0.0090.0000.009
leaves0.0180.0000.018
listEdges0.0150.0000.015
matrix2Graph0.0280.0000.028
mostEdges0.010.000.01
numNoEdges0.0030.0000.004
pancrCaIni0.2690.0000.268
randomEGraph0.0070.0000.007
randomGraph0.0090.0000.009
randomNodeGraph0.0000.0030.004
removeEdge0.0130.0000.013
removeNode0.0090.0000.009
renderInfo-class0.0080.0000.008
reverseEdgeDirections0.0050.0000.005
simpleEdge-class0.0000.0010.001
standardLabeling0.0920.0020.094
subGraph0.0010.0000.002
toDotR-methods0.0300.0000.038
ugraph0.0120.0000.012
validGraph0.0020.0000.001