Multiple platform build/check report for BioC 3.21 - CHECK results for graph on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4658
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4455
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4408
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 nebbiolo1

To the developers/maintainers of the graph package:
- 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 Troubleshooting Build Report for more information.
- 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: 1.85.1

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:graph.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings graph_1.85.1.tar.gz

StartedAt: 2025-01-24 22:51:12 -0500 (Fri, 24 Jan 2025)

EndedAt: 2025-01-24 22:52:19 -0500 (Fri, 24 Jan 2025)

EllapsedTime: 67.1 seconds

RetCode: 1

Status: ERROR

CheckDir: graph.Rcheck

Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:graph.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings graph_1.85.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/graph.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 ‘1.85.1’
* 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 ... 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 $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘graph_unit_tests.R’
 ERROR
Running the tests in ‘tests/graph_unit_tests.R’ failed.
Last 13 lines of output:
   8: all.equal(target, current, tolerance = tolerance, ...)
   9: checkEquals(edges(g1), edges(removeEdge(c0, c0, g1)))
  10: func()
  11: system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest)
  12: doTryCatch(return(expr), name, parentenv, handler)
  13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  14: tryCatchList(expr, classes, parentenv, handlers)
  15: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
  16: try(system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest))
  17: .executeTestCase(funcName, envir = sandbox, setUpFunc = .setUp,     tearDownFunc = .tearDown)
  18: .sourceTestFile(testFile, testSuite$testFuncRegexp)
  19: RUnit::runTestSuite(suite)
  20: BiocGenerics:::testPackage("graph", pattern = "_test.R")
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault (core dumped)
* 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: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/graph.Rcheck/00check.log’
for details.

Installation output

graph.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL graph
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘graph’ ...
** this is package ‘graph’ version ‘1.85.1’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c graph.c -o graph.o
gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o graph.so graph.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
mv graph.so BioC_graph.so
installing to /home/biocbuild/bbs-3.21-bioc/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.fail


R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
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


 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: .remEdge(from, to, graph)
 2: removeEdge(c0, c0, g1)
 3: removeEdge(c0, c0, g1)
 4: edges(removeEdge(c0, c0, g1))
 5: mode(current)
 6: attr.all.equal(target, current, ...)
 7: all.equal.list(target, current, tolerance = tolerance, ...)
 8: all.equal(target, current, tolerance = tolerance, ...)
 9: checkEquals(edges(g1), edges(removeEdge(c0, c0, g1)))
10: func()
11: system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
16: try(system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest))
17: .executeTestCase(funcName, envir = sandbox, setUpFunc = .setUp,     tearDownFunc = .tearDown)
18: .sourceTestFile(testFile, testSuite$testFuncRegexp)
19: RUnit::runTestSuite(suite)
20: BiocGenerics:::testPackage("graph", pattern = "_test.R")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)

Example timings

graph.Rcheck/graph-Ex.timings

name	user	system	elapsed
DFS	0.104	0.001	0.105
IMCA	0.013	0.004	0.016
MAPKsig	0.001	0.001	0.002
MultiGraph-class	0.105	0.016	0.120
acc-methods	0.003	0.001	0.004
addEdge	0.035	0.000	0.034
addNode	0.007	0.000	0.007
adj-methods	0.002	0.000	0.002
adjacencyMatrix	0.001	0.001	0.002
apoptosisGraph	0.001	0.001	0.002
attrData-class	0.000	0.001	0.001
aveNumEdges	0.003	0.000	0.003
biocRepos	0.001	0.000	0.001
boundary	0.001	0.002	0.002
calcProb	0	0	0
calcSumProb	0.004	0.000	0.003
clearNode	0.006	0.000	0.005
clusterGraph-class	0.013	0.000	0.013
clusteringCoefficient-methods	0.027	0.001	0.028
combineNodes	0.062	0.000	0.063
distGraph-class	0.001	0.000	0.001
duplicatedEdges	0	0	0
edgeMatrix	0.006	0.001	0.008
edgeSets	0.028	0.001	0.029
edgeWeights	0.006	0.001	0.008
fromGXL-methods	0.160	0.008	0.168
graph-class	0.018	0.001	0.019
graph2SparseM	0.078	0.000	0.079
graphAM-class	0.014	0.000	0.014
graphBAM-class	0.022	0.000	0.022
graphExamples	0.003	0.001	0.004
graphNEL-class	0.004	0.002	0.006
inEdges	0.005	0.000	0.005
leaves	0.007	0.001	0.007
listEdges	0.006	0.002	0.009
matrix2Graph	0.007	0.001	0.008
mostEdges	0.005	0.000	0.005
numNoEdges	0.002	0.000	0.002
pancrCaIni	0.001	0.000	0.001
randomEGraph	0.003	0.000	0.003
randomGraph	0.002	0.000	0.002
randomNodeGraph	0.001	0.001	0.002
removeEdge	0.007	0.000	0.007
removeNode	0.009	0.000	0.009
renderInfo-class	0.004	0.000	0.005
reverseEdgeDirections	0.003	0.001	0.002
simpleEdge-class	0.001	0.000	0.001
standardLabeling	0.041	0.001	0.043
subGraph	0.001	0.000	0.002
toDotR-methods	0.016	0.002	0.018
ugraph	0.008	0.000	0.007
validGraph	0.001	0.000	0.001