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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:MACSr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MACSr_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MACSr.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 ‘/home/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 loading without being on the library search path ... 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 8.707  0.714  14.371
bdgdiff      7.007  0.212  10.455
refinepeak   6.141  0.111   9.458
bdgcmp       5.896  0.279   9.965
cmbreps      5.659  0.180   9.031
bdgopt       4.628  0.243   8.583
callpeak     4.060  0.171   7.465
* 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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/MACSr.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL MACSr
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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  @ 06 Jul 2024 06:08:55: [617 MB] 
# Command line: 
# ARGUMENTS LIST:
# name = run_callpeak_narrow0
# format = BED
# ChIP-seq file = ['/home/biocbuild/.cache/R/ExperimentHub/19524844b35103_4601']
# control file = ['/home/biocbuild/.cache/R/ExperimentHub/195248408a18a2_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  @ 06 Jul 2024 06:08:55: [617 MB] #1 read tag files... 
INFO  @ 06 Jul 2024 06:08:55: [617 MB] #1 read treatment tags... 
INFO  @ 06 Jul 2024 06:08:56: [624 MB] #1.2 read input tags... 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #1 tag size is determined as 101 bps 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #1 tag size = 101.0 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #1  total tags in treatment: 49622 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #1 user defined the maximum tags... 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #1  tags after filtering in treatment: 48047 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #1  Redundant rate of treatment: 0.03 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #1  total tags in control: 50837 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #1 user defined the maximum tags... 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #1  tags after filtering in control: 50783 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #1  Redundant rate of control: 0.00 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #1 finished! 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #2 Build Peak Model... 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #2 looking for paired plus/minus strand peaks... 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #2 Total number of paired peaks: 469 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #2 Model building with cross-correlation: Done 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #2 finished! 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #2 predicted fragment length is 228 bps 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #2 alternative fragment length(s) may be 228 bps 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #2.2 Generate R script for model : /home/biocbuild/tmp/Rtmpg5Rw08/run_callpeak_narrow0_model.r 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #3 Call peaks... 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #3 Pre-compute pvalue-qvalue table... 
INFO  @ 06 Jul 2024 06:08:56: [628 MB] #3 Cutoff vs peaks called will be analyzed! 
INFO  @ 06 Jul 2024 06:08:57: [649 MB] #3 Analysis of cutoff vs num of peaks or total length has been saved in b'/home/biocbuild/tmp/Rtmpg5Rw08/run_callpeak_narrow0_cutoff_analysis.txt' 
INFO  @ 06 Jul 2024 06:08:57: [649 MB] #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ 06 Jul 2024 06:08:57: [649 MB] #3   Write bedGraph files for treatment pileup (after scaling if necessary)... run_callpeak_narrow0_treat_pileup.bdg 
INFO  @ 06 Jul 2024 06:08:57: [649 MB] #3   Write bedGraph files for control lambda (after scaling if necessary)... run_callpeak_narrow0_control_lambda.bdg 
INFO  @ 06 Jul 2024 06:08:57: [649 MB] #3   Pileup will be based on sequencing depth in treatment. 
INFO  @ 06 Jul 2024 06:08:57: [649 MB] #3 Call peaks for each chromosome... 
INFO  @ 06 Jul 2024 06:08:57: [649 MB] #4 Write output xls file... /home/biocbuild/tmp/Rtmpg5Rw08/run_callpeak_narrow0_peaks.xls 
INFO  @ 06 Jul 2024 06:08:57: [649 MB] #4 Write peak in narrowPeak format file... /home/biocbuild/tmp/Rtmpg5Rw08/run_callpeak_narrow0_peaks.narrowPeak 
INFO  @ 06 Jul 2024 06:08:57: [649 MB] #4 Write summits bed file... /home/biocbuild/tmp/Rtmpg5Rw08/run_callpeak_narrow0_summits.bed 
INFO  @ 06 Jul 2024 06:08:57: [649 MB] Done! 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
 38.943   2.316  49.532