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This page was generated on 2021-11-29 15:05:59 -0500 (Mon, 29 Nov 2021).

CHECK results for MACSr on machv2

To the developers/maintainers of the MACSr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MACSr.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1031/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MACSr 1.2.0  (landing page)
Qiang Hu
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/MACSr
git_branch: RELEASE_3_14
git_last_commit: 78f9ee1
git_last_commit_date: 2021-10-26 13:06:52 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64... NOT SUPPORTED ...
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MACSr
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2021-11-28 17:56:39 -0500 (Sun, 28 Nov 2021)
EndedAt: 2021-11-28 18:02:43 -0500 (Sun, 28 Nov 2021)
EllapsedTime: 364.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MACSr.Rcheck
Warnings: 0

Command output

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### 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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/MACSr.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.2.0’
* 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-3.14-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 16.196  1.306  19.060
refinepeak   12.921  0.212  13.833
bdgdiff      12.109  0.364  13.371
cmbreps      11.652  0.266  12.769
bdgcmp       10.567  0.311  11.706
bdgopt        9.768  0.233  10.750
callpeak      8.931  0.184   9.951
filterdup     4.718  0.101   5.494
predictd      4.692  0.102   5.311
randsample    4.381  0.085   5.054
pileup        4.361  0.101   5.089
* 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-3.14-bioc/meat/MACSr.Rcheck/00check.log’
for details.



Installation output

MACSr.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)

Tests output

MACSr.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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  @ Sun, 28 Nov 2021 18:02:05: 
# Command line: 
# ARGUMENTS LIST:
# name = run_callpeak_narrow0
# format = BED
# ChIP-seq file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/881557b9e561_4601']
# control file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/88156d827045_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  @ Sun, 28 Nov 2021 18:02:05: #1 read tag files... 
INFO  @ Sun, 28 Nov 2021 18:02:05: #1 read treatment tags... 
INFO  @ Sun, 28 Nov 2021 18:02:05: #1.2 read input tags... 
INFO  @ Sun, 28 Nov 2021 18:02:05: #1 tag size is determined as 101 bps 
INFO  @ Sun, 28 Nov 2021 18:02:05: #1 tag size = 101.0 
INFO  @ Sun, 28 Nov 2021 18:02:05: #1  total tags in treatment: 49622 
INFO  @ Sun, 28 Nov 2021 18:02:05: #1 user defined the maximum tags... 
INFO  @ Sun, 28 Nov 2021 18:02:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Sun, 28 Nov 2021 18:02:05: #1  tags after filtering in treatment: 48047 
INFO  @ Sun, 28 Nov 2021 18:02:05: #1  Redundant rate of treatment: 0.03 
INFO  @ Sun, 28 Nov 2021 18:02:05: #1  total tags in control: 50837 
INFO  @ Sun, 28 Nov 2021 18:02:05: #1 user defined the maximum tags... 
INFO  @ Sun, 28 Nov 2021 18:02:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Sun, 28 Nov 2021 18:02:05: #1  tags after filtering in control: 50783 
INFO  @ Sun, 28 Nov 2021 18:02:05: #1  Redundant rate of control: 0.00 
INFO  @ Sun, 28 Nov 2021 18:02:05: #1 finished! 
INFO  @ Sun, 28 Nov 2021 18:02:05: #2 Build Peak Model... 
INFO  @ Sun, 28 Nov 2021 18:02:05: #2 looking for paired plus/minus strand peaks... 
INFO  @ Sun, 28 Nov 2021 18:02:05: #2 Total number of paired peaks: 469 
INFO  @ Sun, 28 Nov 2021 18:02:05: #2 Model building with cross-correlation: Done 
INFO  @ Sun, 28 Nov 2021 18:02:05: #2 finished! 
INFO  @ Sun, 28 Nov 2021 18:02:05: #2 predicted fragment length is 228 bps 
INFO  @ Sun, 28 Nov 2021 18:02:05: #2 alternative fragment length(s) may be 228 bps 
INFO  @ Sun, 28 Nov 2021 18:02:05: #2.2 Generate R script for model : /tmp/Rtmpnxh7Yr/run_callpeak_narrow0_model.r 
INFO  @ Sun, 28 Nov 2021 18:02:05: #3 Call peaks... 
INFO  @ Sun, 28 Nov 2021 18:02:05: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 28 Nov 2021 18:02:05: #3 Cutoff vs peaks called will be analyzed! 
INFO  @ Sun, 28 Nov 2021 18:02:06: #3 Analysis of cutoff vs num of peaks or total length has been saved in b'/tmp/Rtmpnxh7Yr/run_callpeak_narrow0_cutoff_analysis.txt' 
INFO  @ Sun, 28 Nov 2021 18:02:06: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 28 Nov 2021 18:02:06: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... run_callpeak_narrow0_treat_pileup.bdg 
INFO  @ Sun, 28 Nov 2021 18:02:06: #3   Write bedGraph files for control lambda (after scaling if necessary)... run_callpeak_narrow0_control_lambda.bdg 
INFO  @ Sun, 28 Nov 2021 18:02:06: #3   Pileup will be based on sequencing depth in treatment. 
INFO  @ Sun, 28 Nov 2021 18:02:06: #3 Call peaks for each chromosome... 
INFO  @ Sun, 28 Nov 2021 18:02:07: #4 Write output xls file... /tmp/Rtmpnxh7Yr/run_callpeak_narrow0_peaks.xls 
INFO  @ Sun, 28 Nov 2021 18:02:07: #4 Write peak in narrowPeak format file... /tmp/Rtmpnxh7Yr/run_callpeak_narrow0_peaks.narrowPeak 
INFO  @ Sun, 28 Nov 2021 18:02:07: #4 Write summits bed file... /tmp/Rtmpnxh7Yr/run_callpeak_narrow0_summits.bed 
INFO  @ Sun, 28 Nov 2021 18:02:07: Done! 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
 57.468   3.427  63.148 

Example timings

MACSr.Rcheck/MACSr-Ex.timings

nameusersystemelapsed
bdgbroadcall16.196 1.30619.060
bdgcmp10.567 0.31111.706
bdgdiff12.109 0.36413.371
bdgopt 9.768 0.23310.750
bdgpeakcall0.0070.0000.008
callpeak8.9310.1849.951
callvar0.0050.0000.005
cmbreps11.652 0.26612.769
filterdup4.7180.1015.494
pileup4.3610.1015.089
predictd4.6920.1025.311
randsample4.3810.0855.054
refinepeak12.921 0.21213.833