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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MOSim.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MOSim_2.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/MOSim.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-21 06:21:04 UTC
* checking for file ‘MOSim/DESCRIPTION’ ... OK
* this is package ‘MOSim’ version ‘2.8.0’
* package encoding: UTF-8
* 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 ‘MOSim’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘dplyr::count’ by ‘matrixStats::count’ when loading ‘MOSim’
See ‘/home/biocbuild/bbs-3.23-bioc/meat/MOSim.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
* 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 ... NOTE
make_association_dataframe : keep_remaining: no visible binding for
  global variable ‘Freq.a’
make_association_dataframe : keep_remaining: no visible binding for
  global variable ‘Freq.ao’
make_association_dataframe : keep_remaining: no visible binding for
  global variable ‘cluster’
make_association_dataframe : keep_remaining: no visible binding for
  global variable ‘Freq’
make_association_dataframe : keep_remaining2: no visible binding for
  global variable ‘Freq.a’
make_association_dataframe : keep_remaining2: no visible binding for
  global variable ‘Freq.ao’
make_association_dataframe : keep_remaining2: no visible binding for
  global variable ‘cluster’
make_association_dataframe : keep_remaining2: no visible binding for
  global variable ‘Freq’
make_association_dataframe: no visible binding for global variable
  ‘Peak_ID’
make_association_dataframe: no visible binding for global variable
  ‘Gene_ID’
Undefined global functions or variables:
  Freq Freq.a Freq.ao Gene_ID Peak_ID cluster
* checking Rd files ... NOTE
checkRd: (-1) TF_human.Rd:12: Lost braces; missing escapes or markup?
    12 |  @source {https://tflink.net/}
       |          ^
checkRd: (-1) associationList.Rd:14: Lost braces; missing escapes or markup?
    14 |  @source {Created in-house to serve as an example}
       |          ^
checkRd: (-1) sc_mosim.Rd:94: Lost braces; missing escapes or markup?
    94 | {https://tflink.net/}}
       | ^
checkRd: (-1) scatac.Rd:14-15: Lost braces
    14 |  @source {https://github.com/satijalab/seurat-data, we took 11 cells 
       |          ^
checkRd: (-1) scrna.Rd:14-15: Lost braces
    14 |  @source {https://github.com/satijalab/seurat-data, we took 11 cells 
       |          ^
checkRd: (-1) scrna.Rd:23-28: Lost braces
    23 |  for (cell_type in unique_cell_types) {
       |                                       ^
* 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 compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
discretize            73.382  1.134  74.531
omicSettings          71.323  0.435  71.760
omicSim               68.678  0.340  70.539
plotProfile           65.826  0.366  66.198
omicResults           52.761  0.247  53.010
experimentalDesign    49.256  0.258  49.518
mosim                 48.543  0.315  48.863
sc_mosim              41.112  0.317  41.428
sc_omicSettings       34.515  0.198  34.713
sc_omicResults        34.486  0.102  34.589
make_cluster_patterns 13.758  0.099  13.858
* 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 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/MOSim.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL MOSim
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘MOSim’ ...
** this is package ‘MOSim’ version ‘2.8.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c Random_number.cpp -o Random_number.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o MOSim.so Random_number.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-MOSim/00new/MOSim/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘dplyr::count’ by ‘matrixStats::count’ when loading ‘MOSim’
Creating a new generic function for ‘simulate’ in package ‘MOSim’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘dplyr::count’ by ‘matrixStats::count’ when loading ‘MOSim’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘dplyr::count’ by ‘matrixStats::count’ when loading ‘MOSim’
** testing if installed package keeps a record of temporary installation path
* DONE (MOSim)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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(MOSim)
> 
> #test_check("MOSim")
> 
> proc.time()
   user  system elapsed 
  0.324   0.047   0.359