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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings motifcounter_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/motifcounter.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘motifcounter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifcounter’ version ‘1.30.0’
* 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 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 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 9.728  0.122   9.852
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/motifcounter.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL motifcounter
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘motifcounter’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/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 version 4.4.3 (2025-02-28) -- "Trophy Case"
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.

> library(testthat)
> library(motifcounter)
> 
> test_check("motifcounter")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 841 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 841 ]
> 
> proc.time()
   user  system elapsed 
111.554   5.841 117.389