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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scMitoMut.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scMitoMut_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/scMitoMut.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scMitoMut/DESCRIPTION’ ... OK
* this is package ‘scMitoMut’ version ‘1.0.0’
* 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 ‘scMitoMut’ can be installed ... WARNING
Found the following significant warnings:
  Warning: scMitoMut.Rd:3: docType ‘_PACKAGE’ is unrecognized
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/scMitoMut.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.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 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
export_dt: no visible binding for global variable ‘af’
export_dt: no visible binding for global variable ‘fwd_depth’
export_dt: no visible binding for global variable ‘rev_depth’
export_dt: no visible binding for global variable ‘coverage’
export_dt: no visible binding for global variable ‘alt_count’
export_dt: no visible binding for global variable ‘alt_depth’
export_dt: no visible binding for global variable ‘mut_status’
export_dt: no visible binding for global variable ‘cell_barcode’
export_dt: no visible binding for global variable ‘n’
export_dt: no visible binding for global variable ‘loc’
filter_loc: no visible binding for global variable ‘mut_cell_n’
plot_locus: no visible binding for global variable ‘alt_depth’
plot_locus: no visible binding for global variable ‘depth’
plot_locus: no visible binding for global variable ‘af’
plot_locus: no visible binding for global variable ‘highlight’
process_locus_bb: no visible binding for global variable ‘alt_depth’
process_locus_bb: no visible binding for global variable ‘fwd_depth’
process_locus_bb: no visible binding for global variable ‘rev_depth’
process_locus_bm: no visible binding for global variable ‘alt_depth’
process_locus_bm: no visible binding for global variable ‘fwd_depth’
process_locus_bm: no visible binding for global variable ‘rev_depth’
process_locus_summary: no visible binding for global variable
  ‘alt_depth’
process_locus_summary: no visible binding for global variable
  ‘fwd_depth’
process_locus_summary: no visible binding for global variable
  ‘rev_depth’
read_locus: no visible binding for global variable ‘cell_barcode’
read_locus: no visible binding for global variable ‘fwd_depth’
read_locus: no visible binding for global variable ‘rev_depth’
read_locus: no visible binding for global variable ‘coverage’
read_locus: no visible binding for global variable ‘alt’
read_locus: no visible binding for global variable ‘af’
read_mgatk: no visible binding for global variable ‘fwd_depth’
read_mgatk: no visible binding for global variable ‘rev_depth’
Undefined global functions or variables:
  af alt alt_count alt_depth cell_barcode coverage depth fwd_depth
  highlight loc mut_cell_n mut_status n rev_depth
* checking Rd files ... WARNING
prepare_Rd: scMitoMut.Rd:3: docType ‘_PACKAGE’ is unrecognized
* 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 ... WARNING
Undocumented arguments in Rd file 'rm_mtmutObj.Rd'
  ‘envir’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
export_dt        11.594  4.685  23.153
plot_heatmap     11.285  1.859  18.671
plot_af_coverage  4.756  0.336   9.004
get_pval          4.233  0.349   7.644
filter_loc        4.265  0.294   8.525
run_model_fit     4.232  0.235   7.488
* 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: 3 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/scMitoMut.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scMitoMut
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘scMitoMut’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c em_bm.cpp -o em_bm.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c mle_bb.cpp -o mle_bb.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o scMitoMut.so RcppExports.o em_bm.o mle_bb.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-scMitoMut/00new/scMitoMut/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: scMitoMut.Rd:3: docType ‘_PACKAGE’ is unrecognized
*** 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 (scMitoMut)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(scMitoMut)
> 
> test_check("scMitoMut")
chrM.200
chrM.204
chrM.310
chrM.824
chrM.1000
chrM.1001
chrM.1227
chrM.2285
chrM.6081
chrM.9429
chrM.9728
chrM.9804
chrM.9840
chrM.12889
chrM.16093
chrM.16147
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
> 
> proc.time()
   user  system elapsed 
  9.163   0.788  15.283