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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MACSr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MACSr_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MACSr.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MACSr/DESCRIPTION’ ... OK
* this is package ‘MACSr’ version ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
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 ‘MACSr’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/MACSr.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... 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 shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
bdgbroadcall 11.432  1.982  15.685
bdgdiff       7.612  0.407   9.346
refinepeak    6.021  0.280   7.774
cmbreps       5.544  0.311   7.327
bdgcmp        5.002  0.257   6.670
bdgopt        4.415  0.305   6.177
callpeak      3.998  0.285   5.504
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/MACSr.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MACSr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘MACSr’ ...
** using non-staged installation via StagedInstall field
** 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
* DONE (MACSr)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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.

> library(testthat)
> library(MACSr)
> 
> test_check("MACSr")
INFO  @ 28 Jun 2024 00:27:41: [746 MB] 
# Command line: 
# ARGUMENTS LIST:
# name = run_callpeak_narrow0
# format = BED
# ChIP-seq file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/571854168a5_4601']
# control file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/571893d2b55_4606']
# effective genome size = 5.20e+07
# band width = 300
# model fold = [5.0, 50.0]
# qvalue cutoff = 5.00e-02
# The maximum gap between significant sites is assigned as the read length/tag size.
# The minimum length of peaks is assigned as the predicted fragment length "d".
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# Additional cutoff on fold-enrichment is: 0.10
# Paired-End mode is off
 
INFO  @ 28 Jun 2024 00:27:41: [746 MB] #1 read tag files... 
INFO  @ 28 Jun 2024 00:27:41: [746 MB] #1 read treatment tags... 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #1.2 read input tags... 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #1 tag size is determined as 101 bps 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #1 tag size = 101.0 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #1  total tags in treatment: 49622 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #1 user defined the maximum tags... 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #1  tags after filtering in treatment: 48047 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #1  Redundant rate of treatment: 0.03 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #1  total tags in control: 50837 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #1 user defined the maximum tags... 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #1  tags after filtering in control: 50783 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #1  Redundant rate of control: 0.00 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #1 finished! 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #2 Build Peak Model... 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #2 looking for paired plus/minus strand peaks... 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #2 Total number of paired peaks: 469 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #2 Model building with cross-correlation: Done 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #2 finished! 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #2 predicted fragment length is 228 bps 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #2 alternative fragment length(s) may be 228 bps 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #2.2 Generate R script for model : /tmp/Rtmp8269wZ/run_callpeak_narrow0_model.r 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #3 Call peaks... 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #3 Pre-compute pvalue-qvalue table... 
INFO  @ 28 Jun 2024 00:27:41: [752 MB] #3 Cutoff vs peaks called will be analyzed! 
INFO  @ 28 Jun 2024 00:27:42: [777 MB] #3 Analysis of cutoff vs num of peaks or total length has been saved in b'/tmp/Rtmp8269wZ/run_callpeak_narrow0_cutoff_analysis.txt' 
INFO  @ 28 Jun 2024 00:27:42: [777 MB] #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ 28 Jun 2024 00:27:42: [777 MB] #3   Write bedGraph files for treatment pileup (after scaling if necessary)... run_callpeak_narrow0_treat_pileup.bdg 
INFO  @ 28 Jun 2024 00:27:42: [777 MB] #3   Write bedGraph files for control lambda (after scaling if necessary)... run_callpeak_narrow0_control_lambda.bdg 
INFO  @ 28 Jun 2024 00:27:42: [777 MB] #3   Pileup will be based on sequencing depth in treatment. 
INFO  @ 28 Jun 2024 00:27:42: [777 MB] #3 Call peaks for each chromosome... 
INFO  @ 28 Jun 2024 00:27:42: [781 MB] #4 Write output xls file... /tmp/Rtmp8269wZ/run_callpeak_narrow0_peaks.xls 
INFO  @ 28 Jun 2024 00:27:42: [782 MB] #4 Write peak in narrowPeak format file... /tmp/Rtmp8269wZ/run_callpeak_narrow0_peaks.narrowPeak 
INFO  @ 28 Jun 2024 00:27:42: [782 MB] #4 Write summits bed file... /tmp/Rtmp8269wZ/run_callpeak_narrow0_summits.bed 
INFO  @ 28 Jun 2024 00:27:42: [782 MB] Done! 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
 37.759   3.508  43.787