##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings motifcounter_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/motifcounter.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifcounter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifcounter’ version ‘1.32.0’
* 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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 whether startup messages can be suppressed ... 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 11.7  0.028  11.743
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R/bin/BATCH: line 60: 1740938 Bus error               (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  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(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
  25: source_file(path, env = env(env), desc = desc, error_call = error_call)
  26: FUN(X[[i]], ...)
  27: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  28: doTryCatch(return(expr), name, parentenv, handler)
  29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  30: tryCatchList(expr, classes, parentenv, handlers)
  31: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  32: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  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,     desc = desc, load_package = load_package, error_call = error_call)
  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,     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 ...
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/motifcounter.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL motifcounter
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘motifcounter’ ...
** this is package ‘motifcounter’ version ‘1.32.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c Rbackground.c -o Rbackground.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c Rcombinatorial.c -o Rcombinatorial.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c Rcompoundpoisson.c -o Rcompoundpoisson.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c Rminmaxscore.c -o Rminmaxscore.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c Roption.c -o Roption.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c Roverlap.c -o Roverlap.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c Rscore1d.c -o Rscore1d.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -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;
      |                     ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c Rsimulate.c -o Rsimulate.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c background.c -o background.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c combinatorial.c -o combinatorial.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c compoundpoisson.c -o compoundpoisson.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c markovchain.c -o markovchain.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c markovchain_single.c -o markovchain_single.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c matrix.c -o matrix.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c mdist_register.c -o mdist_register.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c minmaxscore.c -o minmaxscore.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c overlap.c -o overlap.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c score1d.c -o score1d.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c score2d.c -o score2d.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -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;
      |                   ^~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c sequence.c -o sequence.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DIN_R -fPIC  -g -O2  -Wall -Werror=format-security -c simulate.c -o simulate.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/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/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-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)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> library(testthat)
> library(motifcounter)
> 
> test_check("motifcounter")

 *** caught bus error ***
address 0xffff00000003, cause 'invalid alignment'

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(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
25: source_file(path, env = env(env), desc = desc, error_call = error_call)
26: FUN(X[[i]], ...)
27: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
32: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
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,     desc = desc, load_package = load_package, error_call = error_call)
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,     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 ...