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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MOSim.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MOSim_2.3.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/MOSim.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MOSim/DESCRIPTION' ... OK
* this is package 'MOSim' version '2.3.0'
* 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 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 'E:/biocbuild/bbs-3.21-bioc/meat/MOSim.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* checking installed package size ... INFO
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
* 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 ... 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 ... NOTE
Note: information on .o files for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/MOSim/libs/x64/MOSim.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
omicSettings          93.50  10.60  104.27
discretize            93.89   6.09   99.99
omicSim               88.73   9.66   98.42
plotProfile           86.86  10.74   97.59
omicResults           67.41   7.29   74.73
mosim                 66.37   7.23   73.63
experimentalDesign    63.60   7.01   70.67
sc_mosim              53.11   1.45   54.85
sc_omicResults        47.25   0.67   47.94
sc_omicSettings       46.68   0.86   47.51
make_cluster_patterns 18.64   0.27   18.95
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/MOSim.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL MOSim
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'MOSim' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/cpp11/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c Random_number.cpp -o Random_number.o
g++ -std=gnu++17 -shared -s -static-libgcc -o MOSim.dll tmp.def Random_number.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-MOSim/00new/MOSim/libs/x64
** 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'
** 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 Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
   0.46    0.01    0.46