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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings motifcounter_1.35.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/motifcounter.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-13 00:52:22 UTC
* using option ‘--no-vignettes’
* checking for file ‘motifcounter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifcounter’ version ‘1.35.1’
* 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 ... 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: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* 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 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 ... INFO
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 ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("motifcounter")
  Saving _problems/testbackground-79.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 840 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('testbackground.R:79:5'): readBackground ─────────────────────────────
  Error in `is_true()`: could not find function "is_true"
  Backtrace:
      ▆
   1. └─testthat::expect_that(...) at testbackground.R:79:5
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 840 ]
  Error:
  ! Test failures.
  Execution halted
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/motifcounter.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL motifcounter
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘motifcounter’ ...
** this is package ‘motifcounter’ version ‘1.35.1’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rbackground.c -o Rbackground.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rcombinatorial.c -o Rcombinatorial.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rcompoundpoisson.c -o Rcompoundpoisson.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rminmaxscore.c -o Rminmaxscore.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Roption.c -o Roption.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Roverlap.c -o Roverlap.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rscore1d.c -o Rscore1d.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rsequence.c -o Rsequence.o
Rsequence.c:143:21: warning: unused variable 'noscores' [-Wunused-variable]
  143 |     int mins, maxs, noscores;
      |                     ^~~~~~~~
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rsimulate.c -o Rsimulate.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c background.c -o background.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c combinatorial.c -o combinatorial.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c compoundpoisson.c -o compoundpoisson.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c markovchain.c -o markovchain.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c markovchain_single.c -o markovchain_single.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c matrix.c -o matrix.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c mdist_register.c -o mdist_register.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c minmaxscore.c -o minmaxscore.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c overlap.c -o overlap.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c score1d.c -o score1d.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c score2d.c -o score2d.o
score2d.c:597:15: warning: variable 'p0' set but not used [-Wunused-but-set-variable]
  597 |     double p, p0 = 0.0, p1 = 0.0, ptmp;
      |               ^
score2d.c:597:25: warning: variable 'p1' set but not used [-Wunused-but-set-variable]
  597 |     double p, p0 = 0.0, p1 = 0.0, ptmp;
      |                         ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c scorefunctions.c -o scorefunctions.o
scorefunctions.c:84:22: warning: unused variable 'cindex' [-Wunused-variable]
   84 |     int j, i, index, cindex, ds;
      |                      ^~~~~~
scorefunctions.c:119:17: warning: unused variable 'cindex' [-Wunused-variable]
  119 |   int s, index, cindex;
      |                 ^~~~~~
scorefunctions.c:159:19: warning: unused variable 'cindex' [-Wunused-variable]
  159 |     int s, index, cindex;
      |                   ^~~~~~
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c sequence.c -o sequence.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c simulate.c -o simulate.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/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
Warning in fun(libname, pkgname) :
  Package 'motifcounter' is deprecated and will be removed from
  Bioconductor version 3.24
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'motifcounter' is deprecated and will be removed from
  Bioconductor version 3.24
** testing if installed package keeps a record of temporary installation path
* DONE (motifcounter)

R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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)
Warning message:
In fun(libname, pkgname) :
  Package 'motifcounter' is deprecated and will be removed from
  Bioconductor version 3.24
> 
> test_check("motifcounter")
Saving _problems/testbackground-79.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 840 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('testbackground.R:79:5'): readBackground ─────────────────────────────
Error in `is_true()`: could not find function "is_true"
Backtrace:
    ▆
 1. └─testthat::expect_that(...) at testbackground.R:79:5

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 840 ]
Error:
! Test failures.
Execution halted