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This page was generated on 2025-04-09 10:24 -0400 (Wed, 09 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88118) -- "How About a Twenty-Six" 869
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Package 107/217HostnameOS / ArchINSTALLBUILDCHECK
graph 1.85.3  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2025-04-09 06:00 -0400 (Wed, 09 Apr 2025)
git_url: https://git.bioconductor.org/packages/graph
git_branch: devel
git_last_commit: 5a3babc
git_last_commit_date: 2025-03-19 09:55:59 -0400 (Wed, 19 Mar 2025)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  


CHECK results for graph on teran2

To the developers/maintainers of the graph package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: graph
Version: 1.85.3
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:graph.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings graph_1.85.3.tar.gz
StartedAt: 2025-04-09 08:35:10 -0400 (Wed, 09 Apr 2025)
EndedAt: 2025-04-09 08:35:59 -0400 (Wed, 09 Apr 2025)
EllapsedTime: 48.3 seconds
RetCode: 0
Status:   OK  
CheckDir: graph.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:graph.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings graph_1.85.3.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/graph.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88118)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ version ‘1.85.3’
* 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
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 code 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'IMCA.Rd':
  ‘[Rgraphviz:plot-methods]{plot.graph}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/graph.Rcheck/00check.log’
for details.


Installation output

graph.Rcheck/00install.out

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### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL graph
###
##############################################################################
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘graph’ ...
** this is package ‘graph’ version ‘1.85.3’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c graph.c -o graph.o
gcc -std=gnu2x -shared -L/usr/local/lib -o graph.so graph.o
mv graph.so BioC_graph.so
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-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 4.5.0 RC (2025-04-04 r88118) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min



RUNIT TEST PROTOCOL -- Wed Apr  9 08:35:39 2025 
*********************************************** 
Number of test functions: 211 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
graph RUnit Tests - 211 test functions, 0 errors, 0 failures
Number of test functions: 211 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  2.367   0.096   2.462 

Example timings

graph.Rcheck/graph-Ex.timings

nameusersystemelapsed
DFS0.0680.0010.069
IMCA0.0090.0070.015
MAPKsig0.0010.0000.002
MultiGraph-class0.0710.0200.091
acc-methods0.0020.0010.003
addEdge0.0230.0000.023
addNode0.0040.0010.005
adj-methods0.0020.0000.002
adjacencyMatrix0.0010.0000.001
apoptosisGraph0.0010.0010.001
attrData-class0.0010.0000.001
aveNumEdges0.0020.0000.002
biocRepos0.0010.0000.002
boundary0.0010.0000.002
calcProb000
calcSumProb0.0020.0000.003
clearNode0.0030.0000.004
clusterGraph-class0.0090.0000.009
clusteringCoefficient-methods0.020.000.02
combineNodes0.0430.0000.044
distGraph-class000
duplicatedEdges0.0010.0000.000
edgeMatrix0.0040.0000.005
edgeSets0.0190.0020.022
edgeWeights0.0050.0000.004
fromGXL-methods0.1160.0120.130
graph-class0.0110.0010.013
graph2SparseM0.0590.0010.060
graphAM-class0.0050.0000.005
graphBAM-class0.0160.0000.016
graphExamples0.0030.0000.003
graphNEL-class0.0040.0000.004
inEdges0.0040.0000.004
leaves0.0040.0010.005
listEdges0.0060.0000.006
matrix2Graph0.0050.0000.006
mostEdges0.0030.0000.003
numNoEdges0.0040.0000.004
pancrCaIni0.0010.0010.001
randomEGraph0.0030.0000.003
randomGraph0.0020.0000.002
randomNodeGraph0.0010.0000.002
removeEdge0.0050.0000.005
removeNode0.0030.0000.004
renderInfo-class0.0030.0000.003
reverseEdgeDirections0.0020.0000.002
simpleEdge-class0.0010.0000.000
standardLabeling0.0280.0000.029
subGraph0.0010.0000.001
toDotR-methods0.0110.0020.014
ugraph0.0050.0000.005
validGraph0.0000.0000.001