##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/MACSr.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MACSr/DESCRIPTION’ ... OK
* this is package ‘MACSr’ version ‘1.4.0’
* 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-3.15-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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 15.576  1.992  18.167
bdgdiff       9.697  0.406  10.609
refinepeak    9.410  0.236  10.038
bdgcmp        8.852  0.408   9.784
cmbreps       7.982  0.338   8.782
bdgopt        5.972  0.282   6.792
callpeak      5.072  0.234   5.800
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/MACSr.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MACSr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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  @ Wed, 19 Oct 2022 04:12:59: 
# Command line: 
# ARGUMENTS LIST:
# name = run_callpeak_narrow0
# format = BED
# ChIP-seq file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/f6b62696b346_4601']
# control file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/f6b66fd3cc74_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  @ Wed, 19 Oct 2022 04:12:59: #1 read tag files... 
INFO  @ Wed, 19 Oct 2022 04:12:59: #1 read treatment tags... 
INFO  @ Wed, 19 Oct 2022 04:12:59: #1.2 read input tags... 
INFO  @ Wed, 19 Oct 2022 04:12:59: #1 tag size is determined as 101 bps 
INFO  @ Wed, 19 Oct 2022 04:12:59: #1 tag size = 101.0 
INFO  @ Wed, 19 Oct 2022 04:12:59: #1  total tags in treatment: 49622 
INFO  @ Wed, 19 Oct 2022 04:12:59: #1 user defined the maximum tags... 
INFO  @ Wed, 19 Oct 2022 04:12:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Wed, 19 Oct 2022 04:12:59: #1  tags after filtering in treatment: 48047 
INFO  @ Wed, 19 Oct 2022 04:12:59: #1  Redundant rate of treatment: 0.03 
INFO  @ Wed, 19 Oct 2022 04:12:59: #1  total tags in control: 50837 
INFO  @ Wed, 19 Oct 2022 04:12:59: #1 user defined the maximum tags... 
INFO  @ Wed, 19 Oct 2022 04:12:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Wed, 19 Oct 2022 04:12:59: #1  tags after filtering in control: 50783 
INFO  @ Wed, 19 Oct 2022 04:12:59: #1  Redundant rate of control: 0.00 
INFO  @ Wed, 19 Oct 2022 04:12:59: #1 finished! 
INFO  @ Wed, 19 Oct 2022 04:12:59: #2 Build Peak Model... 
INFO  @ Wed, 19 Oct 2022 04:12:59: #2 looking for paired plus/minus strand peaks... 
INFO  @ Wed, 19 Oct 2022 04:12:59: #2 Total number of paired peaks: 469 
INFO  @ Wed, 19 Oct 2022 04:12:59: #2 Model building with cross-correlation: Done 
INFO  @ Wed, 19 Oct 2022 04:12:59: #2 finished! 
INFO  @ Wed, 19 Oct 2022 04:12:59: #2 predicted fragment length is 228 bps 
INFO  @ Wed, 19 Oct 2022 04:12:59: #2 alternative fragment length(s) may be 228 bps 
INFO  @ Wed, 19 Oct 2022 04:12:59: #2.2 Generate R script for model : /tmp/RtmpOsdvLu/run_callpeak_narrow0_model.r 
INFO  @ Wed, 19 Oct 2022 04:12:59: #3 Call peaks... 
INFO  @ Wed, 19 Oct 2022 04:12:59: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 19 Oct 2022 04:12:59: #3 Cutoff vs peaks called will be analyzed! 
INFO  @ Wed, 19 Oct 2022 04:13:00: #3 Analysis of cutoff vs num of peaks or total length has been saved in b'/tmp/RtmpOsdvLu/run_callpeak_narrow0_cutoff_analysis.txt' 
INFO  @ Wed, 19 Oct 2022 04:13:00: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 19 Oct 2022 04:13:00: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... run_callpeak_narrow0_treat_pileup.bdg 
INFO  @ Wed, 19 Oct 2022 04:13:00: #3   Write bedGraph files for control lambda (after scaling if necessary)... run_callpeak_narrow0_control_lambda.bdg 
INFO  @ Wed, 19 Oct 2022 04:13:00: #3   Pileup will be based on sequencing depth in treatment. 
INFO  @ Wed, 19 Oct 2022 04:13:00: #3 Call peaks for each chromosome... 
INFO  @ Wed, 19 Oct 2022 04:13:01: #4 Write output xls file... /tmp/RtmpOsdvLu/run_callpeak_narrow0_peaks.xls 
INFO  @ Wed, 19 Oct 2022 04:13:01: #4 Write peak in narrowPeak format file... /tmp/RtmpOsdvLu/run_callpeak_narrow0_peaks.narrowPeak 
INFO  @ Wed, 19 Oct 2022 04:13:01: #4 Write summits bed file... /tmp/RtmpOsdvLu/run_callpeak_narrow0_summits.bed 
INFO  @ Wed, 19 Oct 2022 04:13:01: Done! 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
 58.102   3.964  62.917