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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:compSPOT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings compSPOT_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/compSPOT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘compSPOT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compSPOT’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘compSPOT’ can be installed ... OK
* 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
compare_features : count_mutations_features: no visible binding for
  global variable ‘Sample’
compare_features : count_mutations_features: no visible binding for
  global variable ‘Chromosome’
count_groups: no visible binding for global variable ‘Group’
count_mutations: no visible binding for global variable ‘Sample’
count_mutations: no visible binding for global variable ‘Chromosome’
find_hotspots: no visible binding for global variable ‘percent’
plot_ecdf: no visible binding for global variable ‘Hotspot’
plot_ecdf: no visible binding for global variable ‘Mutation_Count’
plot_ecdf: no visible binding for global variable ‘Group’
plot_features: no visible global function definition for ‘na.omit’
plot_features: no visible binding for global variable ‘Count’
plot_sigspot: no visible binding for global variable ‘percent’
plot_sigspot: no visible binding for global variable ‘number’
plot_sigspot: no visible binding for global variable ‘Label’
plot_sigspot: no visible binding for global variable ‘type’
plot_sigspot: no visible binding for global variable ‘Count’
plot_sigspot: no visible binding for global variable ‘Group’
plot_spot: no visible binding for global variable ‘Mutation_Count’
plot_spot: no visible binding for global variable ‘Hotspot’
plot_spot: no visible binding for global variable ‘Group’
region_counter: no visible binding for global variable ‘Sample’
region_counter: no visible binding for global variable ‘Chromosome’
spot_rank: no visible binding for global variable ‘Chromosome’
Undefined global functions or variables:
  Chromosome Count Group Hotspot Label Mutation_Count Sample na.omit
  number percent type
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
compare_groups 23.557  1.587  25.153
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/compSPOT.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL compSPOT
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘compSPOT’ ...
** using staged installation
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (compSPOT)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(compSPOT)
> 
> test_check("compSPOT")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 202 ]
> 
> proc.time()
   user  system elapsed 
  7.340   0.478   7.822