Back to Build/check report for BioC 3.16
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This page was generated on 2022-06-27 11:05:20 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for graph on nebbiolo2


To the developers/maintainers of the graph package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graph.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 830/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graph 1.75.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-06-26 14:00:03 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/graph
git_branch: master
git_last_commit: b88531e
git_last_commit_date: 2022-04-26 10:54:46 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: graph
Version: 1.75.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:graph.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings graph_1.75.0.tar.gz
StartedAt: 2022-06-26 20:02:38 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 20:03:24 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 45.6 seconds
RetCode: 0
Status:   OK  
CheckDir: graph.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:graph.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings graph_1.75.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/graph.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* 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 ‘1.75.0’
* 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-3.16-bioc/meat/graph.Rcheck/00check.log’
for details.



Installation output

graph.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL graph
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘graph’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c graph.c -o graph.o
gcc -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o graph.so graph.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
mv graph.so BioC_graph.so
installing to /home/biocbuild/bbs-3.16-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 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics"
Copyright (C) 2022 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: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.max, which.min



RUNIT TEST PROTOCOL -- Sun Jun 26 20:03:19 2022 
*********************************************** 
Number of test functions: 208 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
graph RUnit Tests - 208 test functions, 0 errors, 0 failures
Number of test functions: 208 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  3.522   0.092   3.601 

Example timings

graph.Rcheck/graph-Ex.timings

nameusersystemelapsed
DFS0.0310.0000.031
IMCA0.1460.0120.158
MAPKsig0.1030.0000.103
MultiGraph-class0.1210.0000.121
acc-methods0.0070.0000.007
addEdge0.0370.0000.037
addNode0.0090.0000.010
adj-methods0.0020.0000.002
adjacencyMatrix0.0020.0000.002
apoptosisGraph0.0120.0000.012
attrData-class0.0010.0000.001
aveNumEdges0.0030.0000.003
biocRepos0.0010.0000.001
boundary0.0030.0000.002
calcProb000
calcSumProb0.0030.0000.003
clearNode0.0100.0000.009
clusterGraph-class0.0130.0000.013
clusteringCoefficient-methods0.0290.0040.033
combineNodes0.0660.0000.066
distGraph-class0.0000.0000.001
duplicatedEdges000
edgeMatrix0.0070.0000.006
edgeSets0.0280.0000.028
edgeWeights0.0070.0000.007
fromGXL-methods0.2020.0000.202
graph-class0.0030.0000.004
graph2SparseM0.0960.0070.103
graphAM-class0.0080.0000.008
graphBAM-class0.0270.0000.027
graphExamples0.0030.0000.004
graphNEL-class0.0050.0000.006
inEdges0.0140.0000.015
leaves0.0080.0000.008
listEdges0.010.000.01
matrix2Graph0.0220.0000.022
mostEdges0.0050.0000.005
numNoEdges0.0020.0000.002
pancrCaIni0.1290.0080.137
randomEGraph0.0040.0000.004
randomGraph0.0030.0000.002
randomNodeGraph0.0030.0000.002
removeEdge0.0080.0000.007
removeNode0.0060.0000.005
renderInfo-class0.0050.0000.004
reverseEdgeDirections0.0020.0000.003
simpleEdge-class0.0010.0000.001
standardLabeling0.0570.0040.061
subGraph0.0010.0000.001
toDotR-methods0.0150.0040.019
ugraph0.0070.0000.007
validGraph0.0000.0000.001