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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 328/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chipenrich 2.29.0  (landing page)
Kai Wang
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/chipenrich
git_branch: devel
git_last_commit: 32711e6
git_last_commit_date: 2024-04-30 10:33:18 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 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
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for chipenrich on palomino4

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: 2.29.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chipenrich.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings chipenrich_2.29.0.tar.gz
StartedAt: 2024-06-10 00:51:47 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 01:01:21 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 574.5 seconds
RetCode: 0
Status:   OK  
CheckDir: chipenrich.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chipenrich.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings chipenrich_2.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/chipenrich.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'chipenrich/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chipenrich' version '2.29.0'
* 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 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 code 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 8.05   0.42    8.50
polyenrich  7.38   0.30    7.68
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'F:/biocbuild/bbs-3.20-bioc/meat/chipenrich.Rcheck/00check.log'
for details.


Installation output

chipenrich.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL chipenrich
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
 194.00   18.73  213.23 

Example timings

chipenrich.Rcheck/chipenrich-Ex.timings

nameusersystemelapsed
assign_peak_segments0.360.020.52
assign_peaks0.780.000.78
broadenrich8.050.428.50
calc_peak_gene_overlap0.470.020.49
chipenrich2.340.122.48
load_peaks0.060.000.07
num_peaks_per_gene0.430.000.44
peaks2genes0.600.020.62
plot_chipenrich_spline1.300.171.47
plot_dist_to_tss0.290.000.30
plot_gene_coverage0.860.010.87
plot_polyenrich_spline2.060.232.30
polyenrich7.380.307.68
proxReg0.480.030.52
read_bed0.220.030.31
supported_genesets0.020.000.02
supported_genomes000
supported_locusdefs0.010.000.01
supported_methods000
supported_read_lengths0.020.000.02