##############################################################################
##############################################################################
###
### 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/MACSr.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MACSr/DESCRIPTION’ ... OK
* this is package ‘MACSr’ version ‘1.7.0’
* 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-3.17-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 17.737  2.582  27.084
bdgdiff      10.177  0.449  14.870
refinepeak    9.199  0.257  13.443
cmbreps       7.999  0.352  11.690
bdgcmp        8.044  0.306  11.200
bdgopt        6.218  0.323   9.169
callpeak      5.341  0.264   8.044
* 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-3.17-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/4.3/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 Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 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  @ Thu, 16 Mar 2023 03:18:32: 
# 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  @ Thu, 16 Mar 2023 03:18:32: #1 read tag files... 
INFO  @ Thu, 16 Mar 2023 03:18:32: #1 read treatment tags... 
INFO  @ Thu, 16 Mar 2023 03:18:32: #1.2 read input tags... 
INFO  @ Thu, 16 Mar 2023 03:18:32: #1 tag size is determined as 101 bps 
INFO  @ Thu, 16 Mar 2023 03:18:32: #1 tag size = 101.0 
INFO  @ Thu, 16 Mar 2023 03:18:32: #1  total tags in treatment: 49622 
INFO  @ Thu, 16 Mar 2023 03:18:32: #1 user defined the maximum tags... 
INFO  @ Thu, 16 Mar 2023 03:18:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Thu, 16 Mar 2023 03:18:32: #1  tags after filtering in treatment: 48047 
INFO  @ Thu, 16 Mar 2023 03:18:32: #1  Redundant rate of treatment: 0.03 
INFO  @ Thu, 16 Mar 2023 03:18:32: #1  total tags in control: 50837 
INFO  @ Thu, 16 Mar 2023 03:18:32: #1 user defined the maximum tags... 
INFO  @ Thu, 16 Mar 2023 03:18:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Thu, 16 Mar 2023 03:18:32: #1  tags after filtering in control: 50783 
INFO  @ Thu, 16 Mar 2023 03:18:32: #1  Redundant rate of control: 0.00 
INFO  @ Thu, 16 Mar 2023 03:18:32: #1 finished! 
INFO  @ Thu, 16 Mar 2023 03:18:32: #2 Build Peak Model... 
INFO  @ Thu, 16 Mar 2023 03:18:32: #2 looking for paired plus/minus strand peaks... 
INFO  @ Thu, 16 Mar 2023 03:18:32: #2 Total number of paired peaks: 469 
INFO  @ Thu, 16 Mar 2023 03:18:32: #2 Model building with cross-correlation: Done 
INFO  @ Thu, 16 Mar 2023 03:18:32: #2 finished! 
INFO  @ Thu, 16 Mar 2023 03:18:32: #2 predicted fragment length is 228 bps 
INFO  @ Thu, 16 Mar 2023 03:18:32: #2 alternative fragment length(s) may be 228 bps 
INFO  @ Thu, 16 Mar 2023 03:18:32: #2.2 Generate R script for model : /tmp/RtmpHElkz1/run_callpeak_narrow0_model.r 
INFO  @ Thu, 16 Mar 2023 03:18:32: #3 Call peaks... 
INFO  @ Thu, 16 Mar 2023 03:18:32: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 16 Mar 2023 03:18:32: #3 Cutoff vs peaks called will be analyzed! 
INFO  @ Thu, 16 Mar 2023 03:18:34: #3 Analysis of cutoff vs num of peaks or total length has been saved in b'/tmp/RtmpHElkz1/run_callpeak_narrow0_cutoff_analysis.txt' 
INFO  @ Thu, 16 Mar 2023 03:18:34: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Thu, 16 Mar 2023 03:18:34: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... run_callpeak_narrow0_treat_pileup.bdg 
INFO  @ Thu, 16 Mar 2023 03:18:34: #3   Write bedGraph files for control lambda (after scaling if necessary)... run_callpeak_narrow0_control_lambda.bdg 
INFO  @ Thu, 16 Mar 2023 03:18:34: #3   Pileup will be based on sequencing depth in treatment. 
INFO  @ Thu, 16 Mar 2023 03:18:34: #3 Call peaks for each chromosome... 
INFO  @ Thu, 16 Mar 2023 03:18:35: #4 Write output xls file... /tmp/RtmpHElkz1/run_callpeak_narrow0_peaks.xls 
INFO  @ Thu, 16 Mar 2023 03:18:35: #4 Write peak in narrowPeak format file... /tmp/RtmpHElkz1/run_callpeak_narrow0_peaks.narrowPeak 
INFO  @ Thu, 16 Mar 2023 03:18:35: #4 Write summits bed file... /tmp/RtmpHElkz1/run_callpeak_narrow0_summits.bed 
INFO  @ Thu, 16 Mar 2023 03:18:35: Done! 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
 63.396   4.546  90.775