Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-12-05 11:37:29 -0500 (Tue, 05 Dec 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4688
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4421
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4440
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

Package 331/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chipenrich 2.26.0  (landing page)
Kai Wang
Snapshot Date: 2023-12-04 14:05:07 -0500 (Mon, 04 Dec 2023)
git_url: https://git.bioconductor.org/packages/chipenrich
git_branch: RELEASE_3_18
git_last_commit: 8330eab
git_last_commit_date: 2023-10-24 09:55:43 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for chipenrich on lconway


To the developers/maintainers of the chipenrich package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chipenrich.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: chipenrich
Version: 2.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chipenrich.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chipenrich_2.26.0.tar.gz
StartedAt: 2023-12-04 19:12:09 -0500 (Mon, 04 Dec 2023)
EndedAt: 2023-12-04 19:20:56 -0500 (Mon, 04 Dec 2023)
EllapsedTime: 526.8 seconds
RetCode: 0
Status:   OK  
CheckDir: chipenrich.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chipenrich.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chipenrich_2.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/chipenrich.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chipenrich/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chipenrich’ version ‘2.26.0’
* 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 ‘chipenrich’ 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 ... NOTE
checkRd: (-1) broadenrich.Rd:134: Escaped LaTeX specials: \&
checkRd: (-1) chipenrich.Rd:148: Escaped LaTeX specials: \&
checkRd: (-1) hybridenrich.Rd:111: Escaped LaTeX specials: \&
checkRd: (-1) polyenrich.Rd:148: Escaped LaTeX specials: \&
checkRd: (-1) proxReg.Rd:117: Escaped LaTeX specials: \&
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
broadenrich 7.308  0.535   7.899
polyenrich  5.180  0.462   5.685
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/chipenrich.Rcheck/00check.log’
for details.



Installation output

chipenrich.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘chipenrich’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (chipenrich)

Tests output

chipenrich.Rcheck/tests/testthat.Rout


R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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(chipenrich)





> 
> test_check("chipenrich")
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 170 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_5_chipenrich.R:199:1', 'test_5_chipenrich.R:232:1',
  'test_5_chipenrich.R:236:1'

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 170 ]
> 
> proc.time()
   user  system elapsed 
174.064  12.111 188.098 

Example timings

chipenrich.Rcheck/chipenrich-Ex.timings

nameusersystemelapsed
assign_peak_segments0.3810.0170.400
assign_peaks0.5440.0130.561
broadenrich7.3080.5357.899
calc_peak_gene_overlap0.3110.0080.320
chipenrich1.4610.1171.585
load_peaks0.0650.0010.066
num_peaks_per_gene0.4990.0070.509
peaks2genes0.4890.0160.508
plot_chipenrich_spline1.4020.1211.532
plot_dist_to_tss0.3910.0180.411
plot_gene_coverage0.7930.0210.820
plot_polyenrich_spline2.5570.2442.818
polyenrich5.1800.4625.685
proxReg0.5440.0200.567
read_bed0.2780.0070.288
supported_genesets0.0070.0020.009
supported_genomes0.0020.0010.003
supported_locusdefs0.0050.0020.008
supported_methods0.0010.0000.002
supported_read_lengths0.0060.0020.008