Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:05:17 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for MACSr on nebbiolo2


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: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
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 20.04.4 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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MACSr.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MACSr_1.2.0.tar.gz
StartedAt: 2022-01-16 08:29:26 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 08:33:05 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 219.4 seconds
RetCode: 0
Status:   OK  
CheckDir: MACSr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MACSr.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MACSr_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/MACSr.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (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 ‘/home/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 9.637  0.584  10.862
bdgdiff      7.847  0.192   8.533
refinepeak   7.568  0.131   8.061
cmbreps      6.810  0.148   7.427
bdgcmp       6.623  0.156   7.243
bdgopt       6.459  0.124   6.995
callpeak     5.726  0.091   6.283
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/MACSr.Rcheck/00check.log’
for details.



Installation output

MACSr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL MACSr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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-pc-linux-gnu (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, 16 Jan 2022 08:32:48: 
# Command line: 
# ARGUMENTS LIST:
# name = run_callpeak_narrow0
# format = BED
# ChIP-seq file = ['/home/biocbuild/.cache/R/ExperimentHub/3d73832332a552_4601']
# control file = ['/home/biocbuild/.cache/R/ExperimentHub/3d73831c5d77a3_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, 16 Jan 2022 08:32:48: #1 read tag files... 
INFO  @ Sun, 16 Jan 2022 08:32:48: #1 read treatment tags... 
INFO  @ Sun, 16 Jan 2022 08:32:48: #1.2 read input tags... 
INFO  @ Sun, 16 Jan 2022 08:32:48: #1 tag size is determined as 101 bps 
INFO  @ Sun, 16 Jan 2022 08:32:48: #1 tag size = 101.0 
INFO  @ Sun, 16 Jan 2022 08:32:48: #1  total tags in treatment: 49622 
INFO  @ Sun, 16 Jan 2022 08:32:48: #1 user defined the maximum tags... 
INFO  @ Sun, 16 Jan 2022 08:32:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Sun, 16 Jan 2022 08:32:48: #1  tags after filtering in treatment: 48047 
INFO  @ Sun, 16 Jan 2022 08:32:48: #1  Redundant rate of treatment: 0.03 
INFO  @ Sun, 16 Jan 2022 08:32:48: #1  total tags in control: 50837 
INFO  @ Sun, 16 Jan 2022 08:32:48: #1 user defined the maximum tags... 
INFO  @ Sun, 16 Jan 2022 08:32:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Sun, 16 Jan 2022 08:32:48: #1  tags after filtering in control: 50783 
INFO  @ Sun, 16 Jan 2022 08:32:48: #1  Redundant rate of control: 0.00 
INFO  @ Sun, 16 Jan 2022 08:32:48: #1 finished! 
INFO  @ Sun, 16 Jan 2022 08:32:48: #2 Build Peak Model... 
INFO  @ Sun, 16 Jan 2022 08:32:48: #2 looking for paired plus/minus strand peaks... 
INFO  @ Sun, 16 Jan 2022 08:32:48: #2 Total number of paired peaks: 469 
INFO  @ Sun, 16 Jan 2022 08:32:48: #2 Model building with cross-correlation: Done 
INFO  @ Sun, 16 Jan 2022 08:32:48: #2 finished! 
INFO  @ Sun, 16 Jan 2022 08:32:48: #2 predicted fragment length is 228 bps 
INFO  @ Sun, 16 Jan 2022 08:32:48: #2 alternative fragment length(s) may be 228 bps 
INFO  @ Sun, 16 Jan 2022 08:32:48: #2.2 Generate R script for model : /tmp/RtmpokBnH9/run_callpeak_narrow0_model.r 
INFO  @ Sun, 16 Jan 2022 08:32:48: #3 Call peaks... 
INFO  @ Sun, 16 Jan 2022 08:32:48: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 16 Jan 2022 08:32:48: #3 Cutoff vs peaks called will be analyzed! 
INFO  @ Sun, 16 Jan 2022 08:32:49: #3 Analysis of cutoff vs num of peaks or total length has been saved in b'/tmp/RtmpokBnH9/run_callpeak_narrow0_cutoff_analysis.txt' 
INFO  @ Sun, 16 Jan 2022 08:32:49: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 16 Jan 2022 08:32:49: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... run_callpeak_narrow0_treat_pileup.bdg 
INFO  @ Sun, 16 Jan 2022 08:32:49: #3   Write bedGraph files for control lambda (after scaling if necessary)... run_callpeak_narrow0_control_lambda.bdg 
INFO  @ Sun, 16 Jan 2022 08:32:49: #3   Pileup will be based on sequencing depth in treatment. 
INFO  @ Sun, 16 Jan 2022 08:32:49: #3 Call peaks for each chromosome... 
INFO  @ Sun, 16 Jan 2022 08:32:49: #4 Write output xls file... /tmp/RtmpokBnH9/run_callpeak_narrow0_peaks.xls 
INFO  @ Sun, 16 Jan 2022 08:32:49: #4 Write peak in narrowPeak format file... /tmp/RtmpokBnH9/run_callpeak_narrow0_peaks.narrowPeak 
INFO  @ Sun, 16 Jan 2022 08:32:49: #4 Write summits bed file... /tmp/RtmpokBnH9/run_callpeak_narrow0_summits.bed 
INFO  @ Sun, 16 Jan 2022 08:32:49: Done! 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
 35.840   1.733  38.676 

Example timings

MACSr.Rcheck/MACSr-Ex.timings

nameusersystemelapsed
bdgbroadcall 9.637 0.58410.862
bdgcmp6.6230.1567.243
bdgdiff7.8470.1928.533
bdgopt6.4590.1246.995
bdgpeakcall0.0030.0000.003
callpeak5.7260.0916.283
callvar0.0030.0000.003
cmbreps6.8100.1487.427
filterdup3.4870.0763.933
pileup3.3450.0563.768
predictd3.2920.0433.712
randsample3.2800.0563.707
refinepeak7.5680.1318.061