| Back to Rapid builds (Linux only) of a subset of BioC 3.21 Report updated every 6 hours |
This page was generated on 2025-01-10 15:29 -0500 (Fri, 10 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-12-18 r87448) -- "Unsuffered Consequences" | 863 |
| 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 | ||||
| Package 107/216 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| graph 1.85.1 (landing page) Bioconductor Package Maintainer
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||
|
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. |
| Package: graph |
| Version: 1.85.1 |
| 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_1.85.1.tar.gz |
| StartedAt: 2025-01-10 14:23:47 -0500 (Fri, 10 Jan 2025) |
| EndedAt: 2025-01-10 14:24:36 -0500 (Fri, 10 Jan 2025) |
| EllapsedTime: 49.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: graph.Rcheck |
| Warnings: NA |
##############################################################################
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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_1.85.1.tar.gz
###
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##############################################################################
* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/graph.Rcheck’
* using R Under development (unstable) (2024-12-18 r87448)
* 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
‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/graph.Rcheck/00check.log’
for details.
graph.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL graph ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’ * installing *source* package ‘graph’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -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 -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)
graph.Rcheck/tests/graph_unit_tests.Rout.fail
R Under development (unstable) (2024-12-18 r87448) -- "Unsuffered Consequences"
Copyright (C) 2024 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)
graph.Rcheck/graph-Ex.timings
| name | user | system | elapsed | |
| DFS | 0.085 | 0.000 | 0.085 | |
| IMCA | 0.007 | 0.008 | 0.015 | |
| MAPKsig | 0.001 | 0.000 | 0.001 | |
| MultiGraph-class | 0.082 | 0.014 | 0.095 | |
| acc-methods | 0.002 | 0.000 | 0.002 | |
| addEdge | 0.022 | 0.001 | 0.023 | |
| addNode | 0.005 | 0.000 | 0.005 | |
| adj-methods | 0.002 | 0.000 | 0.002 | |
| adjacencyMatrix | 0.000 | 0.000 | 0.001 | |
| apoptosisGraph | 0.001 | 0.002 | 0.002 | |
| attrData-class | 0.001 | 0.000 | 0.001 | |
| aveNumEdges | 0.002 | 0.000 | 0.002 | |
| biocRepos | 0.001 | 0.001 | 0.001 | |
| boundary | 0.002 | 0.000 | 0.002 | |
| calcProb | 0 | 0 | 0 | |
| calcSumProb | 0.003 | 0.000 | 0.003 | |
| clearNode | 0.004 | 0.000 | 0.004 | |
| clusterGraph-class | 0.009 | 0.000 | 0.009 | |
| clusteringCoefficient-methods | 0.021 | 0.000 | 0.021 | |
| combineNodes | 0.043 | 0.000 | 0.043 | |
| distGraph-class | 0 | 0 | 0 | |
| duplicatedEdges | 0 | 0 | 0 | |
| edgeMatrix | 0.004 | 0.001 | 0.005 | |
| edgeSets | 0.020 | 0.001 | 0.022 | |
| edgeWeights | 0.004 | 0.000 | 0.004 | |
| fromGXL-methods | 0.111 | 0.006 | 0.121 | |
| graph-class | 0.017 | 0.000 | 0.017 | |
| graph2SparseM | 0.054 | 0.004 | 0.058 | |
| graphAM-class | 0.006 | 0.001 | 0.006 | |
| graphBAM-class | 0.014 | 0.003 | 0.017 | |
| graphExamples | 0.009 | 0.001 | 0.010 | |
| graphNEL-class | 0.004 | 0.000 | 0.004 | |
| inEdges | 0.004 | 0.000 | 0.003 | |
| leaves | 0.003 | 0.002 | 0.006 | |
| listEdges | 0.005 | 0.000 | 0.006 | |
| matrix2Graph | 0.005 | 0.000 | 0.005 | |
| mostEdges | 0.004 | 0.000 | 0.003 | |
| numNoEdges | 0.001 | 0.000 | 0.002 | |
| pancrCaIni | 0.001 | 0.000 | 0.001 | |
| randomEGraph | 0.003 | 0.000 | 0.002 | |
| randomGraph | 0.002 | 0.000 | 0.002 | |
| randomNodeGraph | 0.001 | 0.000 | 0.002 | |
| removeEdge | 0.005 | 0.000 | 0.005 | |
| removeNode | 0.003 | 0.000 | 0.004 | |
| renderInfo-class | 0.003 | 0.000 | 0.003 | |
| reverseEdgeDirections | 0.002 | 0.000 | 0.002 | |
| simpleEdge-class | 0.001 | 0.000 | 0.000 | |
| standardLabeling | 0.028 | 0.001 | 0.029 | |
| subGraph | 0.000 | 0.000 | 0.001 | |
| toDotR-methods | 0.011 | 0.003 | 0.014 | |
| ugraph | 0.010 | 0.000 | 0.009 | |
| validGraph | 0.001 | 0.000 | 0.000 | |