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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_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MACSr.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MACSr/DESCRIPTION’ ... OK
* this is package ‘MACSr’ version ‘1.13.0’
* 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-3.20-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 9.993  2.614  13.555
bdgdiff      5.685  0.461   6.559
refinepeak   4.892  0.305   5.471
cmbreps      4.533  0.387   5.219
* 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-3.20-bioc/meat/MACSr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MACSr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 4.4.1 RC (2024-06-06 r86719) -- "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.

> library(testthat)
> library(MACSr)
> 
> test_check("MACSr")
INFO  @ 02 Jul 2024 21:13:58: [737 MB] 
# Command line: 
# ARGUMENTS LIST:
# name = run_callpeak_narrow0
# format = BED
# ChIP-seq file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/6c9014553bbb_4601']
# control file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/6c9067c47c6a_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  @ 02 Jul 2024 21:13:58: [737 MB] #1 read tag files... 
INFO  @ 02 Jul 2024 21:13:58: [737 MB] #1 read treatment tags... 
INFO  @ 02 Jul 2024 21:13:58: [744 MB] #1.2 read input tags... 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #1 tag size is determined as 101 bps 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #1 tag size = 101.0 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #1  total tags in treatment: 49622 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #1 user defined the maximum tags... 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #1  tags after filtering in treatment: 48047 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #1  Redundant rate of treatment: 0.03 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #1  total tags in control: 50837 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #1 user defined the maximum tags... 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #1  tags after filtering in control: 50783 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #1  Redundant rate of control: 0.00 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #1 finished! 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #2 Build Peak Model... 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #2 looking for paired plus/minus strand peaks... 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #2 Total number of paired peaks: 469 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #2 Model building with cross-correlation: Done 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #2 finished! 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #2 predicted fragment length is 228 bps 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #2 alternative fragment length(s) may be 228 bps 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #2.2 Generate R script for model : /tmp/RtmpilBlaj/run_callpeak_narrow0_model.r 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #3 Call peaks... 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #3 Pre-compute pvalue-qvalue table... 
INFO  @ 02 Jul 2024 21:13:59: [747 MB] #3 Cutoff vs peaks called will be analyzed! 
INFO  @ 02 Jul 2024 21:13:59: [786 MB] #3 Analysis of cutoff vs num of peaks or total length has been saved in b'/tmp/RtmpilBlaj/run_callpeak_narrow0_cutoff_analysis.txt' 
INFO  @ 02 Jul 2024 21:13:59: [786 MB] #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ 02 Jul 2024 21:13:59: [786 MB] #3   Write bedGraph files for treatment pileup (after scaling if necessary)... run_callpeak_narrow0_treat_pileup.bdg 
INFO  @ 02 Jul 2024 21:13:59: [786 MB] #3   Write bedGraph files for control lambda (after scaling if necessary)... run_callpeak_narrow0_control_lambda.bdg 
INFO  @ 02 Jul 2024 21:13:59: [786 MB] #3   Pileup will be based on sequencing depth in treatment. 
INFO  @ 02 Jul 2024 21:13:59: [786 MB] #3 Call peaks for each chromosome... 
INFO  @ 02 Jul 2024 21:14:00: [798 MB] #4 Write output xls file... /tmp/RtmpilBlaj/run_callpeak_narrow0_peaks.xls 
INFO  @ 02 Jul 2024 21:14:00: [798 MB] #4 Write peak in narrowPeak format file... /tmp/RtmpilBlaj/run_callpeak_narrow0_peaks.narrowPeak 
INFO  @ 02 Jul 2024 21:14:00: [798 MB] #4 Write summits bed file... /tmp/RtmpilBlaj/run_callpeak_narrow0_summits.bed 
INFO  @ 02 Jul 2024 21:14:00: [798 MB] Done! 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
 35.273   4.581  40.906