Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-08-15 13:22:48 -0400 (Mon, 15 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4365
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4118
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4183
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 EpiCompare on merida1


To the developers/maintainers of the EpiCompare package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EpiCompare.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 606/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EpiCompare 1.0.0  (landing page)
Sera Choi
Snapshot Date: 2022-08-14 13:55:13 -0400 (Sun, 14 Aug 2022)
git_url: https://git.bioconductor.org/packages/EpiCompare
git_branch: RELEASE_3_15
git_last_commit: fba3043
git_last_commit_date: 2022-04-27 15:48:02 -0400 (Wed, 27 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: EpiCompare
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EpiCompare_1.0.0.tar.gz
StartedAt: 2022-08-15 01:55:15 -0400 (Mon, 15 Aug 2022)
EndedAt: 2022-08-15 02:08:03 -0400 (Mon, 15 Aug 2022)
EllapsedTime: 767.7 seconds
RetCode: 0
Status:   OK  
CheckDir: EpiCompare.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EpiCompare_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/EpiCompare.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 ‘EpiCompare/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EpiCompare’ version ‘1.0.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘EpiCompare’ can be installed ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
EpiCompare 7.778  0.502    8.47
* 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: OK


Installation output

EpiCompare.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘EpiCompare’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package keeps a record of temporary installation path
* DONE (EpiCompare)

Tests output

EpiCompare.Rcheck/tests/testthat.Rout


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(EpiCompare)


Warning message:
replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' 
> 
> test_check("EpiCompare")
Saving 10 x 7 in image
Rows: 2 Columns: 9
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (3): X1, X4, X6
dbl (5): X2, X3, X5, X7, X8

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2 Columns: 9
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (3): X1, X4, X6
dbl (5): X2, X3, X5, X7, X8

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Working on: CnT
Working on: CnR
Saving 9 x 5 in image
Saving 10 x 10 in image
Saving 10 x 10 in image
Saving 10 x 7 in image
Saving 10 x 7 in image
Writing ==> /tmp/RtmpMbkcML/processed_results/encode_H3K27ac.narrowPeaks.bed
Writing ==> /tmp/RtmpMbkcML/processed_results/CnT_H3K27ac.narrowPeaks.bed
Writing ==> /tmp/RtmpMbkcML/processed_results/CnR_H3K27ac.narrowPeaks.bed
Searching for *.narrowPeaks.bed$ files...
3 matching files identified.
Constructing file names.
Importing files.
/tmp/RtmpMbkcML/processed_results/CnR_H3K27ac.narrowPeaks.bed

/tmp/RtmpMbkcML/processed_results/CnT_H3K27ac.narrowPeaks.bed

/tmp/RtmpMbkcML/processed_results/encode_H3K27ac.narrowPeaks.bed

Writing ==> /tmp/RtmpMbkcML/processed_results/encode_H3K27ac.narrowPeaks.bed
Saving 10 x 7 in image
Saving 10 x 7 in image
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 45 ]
> 
> proc.time()
   user  system elapsed 
173.746   7.822 186.784 

Example timings

EpiCompare.Rcheck/EpiCompare-Ex.timings

nameusersystemelapsed
EpiCompare7.7780.5028.470
fragment_info0.0040.0050.009
gather_files3.7100.0633.784
overlap_heatmap0.2300.0100.241
overlap_percent0.1750.0080.183
overlap_stat_plot0.3200.0110.335
overlap_upset_plot0.9120.0090.925
peak_info1.5240.0991.626
plot_ChIPseeker_annotation0.0410.0060.046
plot_chromHMM0.0400.0060.046
plot_enrichment0.0410.0050.047
tidy_peakfile0.7880.0430.834
tss_plot0.0400.0070.046
width_boxplot0.0770.0070.084
write_example_peaks0.3730.0150.391