| Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-01 07:38:45 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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 | ||||
|
To the developers/maintainers of the motifcounter package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifcounter.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. |
| Package 1244/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| motifcounter 1.23.0 (landing page) Wolfgang Kopp
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: motifcounter |
| Version: 1.23.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings motifcounter_1.23.0.tar.gz |
| StartedAt: 2023-02-28 08:53:47 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 08:59:10 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 322.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: motifcounter.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings motifcounter_1.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/motifcounter.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘motifcounter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifcounter’ version ‘1.23.0’
* 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 ... NOTE
Found the following hidden files and directories:
.zenodo.json
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘motifcounter’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 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 ... 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 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 $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
simulateClumpSizeDist 11.682 0.07 11.752
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
24: test_code(NULL, exprs, env)
25: source_file(path, child_env(env), wrap = wrap)
26: FUN(X[[i]], ...)
27: lapply(test_paths, test_one_file, env = env, wrap = wrap)
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
32: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
33: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package)
34: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel)
35: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
36: test_check("motifcounter")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘motifcounter.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/motifcounter.Rcheck/00check.log’
for details.
motifcounter.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL motifcounter
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘motifcounter’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c Rbackground.c -o Rbackground.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c Rcombinatorial.c -o Rcombinatorial.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c Rcompoundpoisson.c -o Rcompoundpoisson.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c Rminmaxscore.c -o Rminmaxscore.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c Roption.c -o Roption.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c Roverlap.c -o Roverlap.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c Rscore1d.c -o Rscore1d.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c Rsequence.c -o Rsequence.o
Rsequence.c: In function ‘RscoreHistogram’:
Rsequence.c:143:21: warning: unused variable ‘noscores’ [-Wunused-variable]
143 | int mins, maxs, noscores;
| ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c Rsimulate.c -o Rsimulate.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c background.c -o background.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c combinatorial.c -o combinatorial.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c compoundpoisson.c -o compoundpoisson.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c markovchain.c -o markovchain.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c markovchain_single.c -o markovchain_single.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c matrix.c -o matrix.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c mdist_register.c -o mdist_register.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c minmaxscore.c -o minmaxscore.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c overlap.c -o overlap.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c score1d.c -o score1d.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c score2d.c -o score2d.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c scorefunctions.c -o scorefunctions.o
scorefunctions.c: In function ‘getPositionWeights’:
scorefunctions.c:84:22: warning: unused variable ‘cindex’ [-Wunused-variable]
84 | int j, i, index, cindex, ds;
| ^~~~~~
scorefunctions.c: In function ‘hitSequence’:
scorefunctions.c:119:17: warning: unused variable ‘cindex’ [-Wunused-variable]
119 | int s, index, cindex;
| ^~~~~~
scorefunctions.c: In function ‘scoreSequence’:
scorefunctions.c:159:19: warning: unused variable ‘cindex’ [-Wunused-variable]
159 | int s, index, cindex;
| ^~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c sequence.c -o sequence.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -g -O2 -Wall -c simulate.c -o simulate.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o motifcounter.so Rbackground.o Rcombinatorial.o Rcompoundpoisson.o Rminmaxscore.o Roption.o Roverlap.o Rscore1d.o Rsequence.o Rsimulate.o background.o combinatorial.o compoundpoisson.o markovchain.o markovchain_single.o matrix.o mdist_register.o minmaxscore.o overlap.o score1d.o score2d.o scorefunctions.o sequence.o simulate.o -fopenmp -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-motifcounter/00new/motifcounter/libs
** R
** 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 (motifcounter)
motifcounter.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> library(testthat)
> library(motifcounter)
>
> test_check("motifcounter")
*** caught segfault ***
address 0xffff0000005b, cause 'memory not mapped'
Traceback:
1: scoreDist(as.matrix(motif[, 1]), bg)
2: eval(code, test_env)
3: eval(code, test_env)
4: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
12: test_code(desc, code, env = parent.frame(), reporter = reporter)
13: test_that("scoreDists", { alpha = 0.01 motifcounterOptions(alpha) seqfile = system.file("extdata", "seq.fasta", package = "motifcounter") seqs = Biostrings::readDNAStringSet(seqfile) bg = readBackground(seqs, 0) motifname = "x1.tab" motiffile = system.file("extdata", motifname, package = "motifcounter") motif = t(as.matrix(read.table(motiffile))) bg = readBackground(seqs, 2) expect_error(scoreDist(as.matrix(motif[, 1]), bg)) bg = readBackground(seqs, 0) s = round((log(motif[, 1]) - log(bg@station)) * 10) srange = seq(min(s), max(s)) p = rep(0, length(srange)) for (i in 1:length(srange)) { p[i] = sum(bg@station[which(s == srange[i])]) } dp = scoreDist(as.matrix(motif[, 1]), bg) expect_equal(sum(dp[[2]]), 1) expect_equal(length(srange), length(dp[[1]])) expect_equal(srange, round(dp[[1]] * 10)) expect_equal(p, dp[[2]]) for (m in seq(0, 3)) { bg = readBackground(seqs, m) if (m == 0) { sims = scoreDistEmpirical(as.matrix(motif[, 1]), bg, 1, 1000) dp = scoreDist(as.matrix(motif[, 1]), bg) bf = scoreDistBf(as.matrix(motif[, 1]), bg) } else { sims = scoreDistEmpirical(as.matrix(motif[, 1:m]), bg, m, 1000) dp = scoreDist(as.matrix(motif[, 1:m]), bg) bf = scoreDistBf(as.matrix(motif[, 1:m]), bg) } expect_equal(sum(dp[[2]]), 1) expect_equal(bf[[1]], dp[[1]]) expect_equal(bf[[2]], dp[[2]]) expect_equal(sims[[1]], dp[[1]]) expect_equal(sum(sims[[2]][dp[[2]] == 0]), 0) } for (m in seq(1, 3)) { bg = readBackground(seqs, m) dp = scoreDist(motif[, 1:(m + 1)], bg) bf = scoreDistBf(motif[, 1:(m + 1)], bg) sims = scoreDistEmpirical(motif[, 1:(m + 1)], bg, m + 1, 1000) expect_equal(sum(dp[[2]]), 1) expect_equal(bf[[1]], dp[[1]]) expect_equal(bf[[2]], dp[[2]]) expect_equal(sims[[1]], dp[[1]]) expect_equal(sum(sims[[2]][dp[[2]] == 0]), 0) }})
14: eval(code, test_env)
15: eval(code, test_env)
16: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
24: test_code(NULL, exprs, env)
25: source_file(path, child_env(env), wrap = wrap)
26: FUN(X[[i]], ...)
27: lapply(test_paths, test_one_file, env = env, wrap = wrap)
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
32: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
33: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package)
34: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel)
35: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
36: test_check("motifcounter")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
motifcounter.Rcheck/motifcounter-Ex.timings
| name | user | system | elapsed | |
| clumpSizeDist | 0.171 | 0.028 | 0.200 | |
| combinatorialDist | 0.327 | 0.012 | 0.338 | |
| compoundPoissonDist | 0.220 | 0.016 | 0.235 | |
| computeClumpStartProb | 0.158 | 0.004 | 0.162 | |
| generateDNAString | 0.101 | 0.000 | 0.101 | |
| generateDNAStringSet | 0.151 | 0.000 | 0.151 | |
| hitStrand | 0.099 | 0.000 | 0.100 | |
| lenSequences | 0.093 | 0.004 | 0.096 | |
| markovModel | 0.141 | 0.008 | 0.148 | |
| motifAndBackgroundValid | 0.095 | 0.001 | 0.095 | |
| motifEnrichment | 3.422 | 0.000 | 3.422 | |
| motifHitProfile | 0.089 | 0.016 | 0.105 | |
| motifHits | 0.097 | 0.003 | 0.101 | |
| motifValid | 0.001 | 0.001 | 0.001 | |
| motifcounter-package | 1.146 | 0.027 | 1.174 | |
| motifcounterOptions | 0 | 0 | 0 | |
| normalizeMotif | 0.002 | 0.000 | 0.001 | |
| numMotifHits | 0.709 | 0.000 | 0.709 | |
| probOverlapHit | 0.182 | 0.000 | 0.182 | |
| readBackground | 0.092 | 0.000 | 0.093 | |
| revcompMotif | 0.001 | 0.000 | 0.002 | |
| scoreDist | 0.095 | 0.000 | 0.095 | |
| scoreDistBf | 0.119 | 0.000 | 0.119 | |
| scoreDistEmpirical | 2.723 | 0.011 | 2.736 | |
| scoreHistogram | 0.246 | 0.001 | 0.246 | |
| scoreHistogramSingleSeq | 0.101 | 0.000 | 0.101 | |
| scoreProfile | 0.527 | 0.000 | 0.527 | |
| scoreSequence | 0.097 | 0.000 | 0.097 | |
| scoreStrand | 0.097 | 0.000 | 0.097 | |
| scoreThreshold | 0.095 | 0.000 | 0.095 | |
| sigLevel | 0 | 0 | 0 | |
| simulateClumpSizeDist | 11.682 | 0.070 | 11.752 | |
| simulateNumHitsDist | 2.277 | 0.031 | 2.310 | |