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This page was generated on 2021-09-20 15:04:45 -0400 (Mon, 20 Sep 2021).

CHECK results for chipenrich on nebbiolo1

To the developers/maintainers of the chipenrich package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 292/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chipenrich 2.16.0  (landing page)
Raymond G. Cavalcante
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/chipenrich
git_branch: RELEASE_3_13
git_last_commit: 4653bc8
git_last_commit_date: 2021-05-19 12:00:32 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: chipenrich
Version: 2.16.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:chipenrich.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings chipenrich_2.16.0.tar.gz
StartedAt: 2021-09-19 09:11:21 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 09:18:05 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 404.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: chipenrich.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:chipenrich.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings chipenrich_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/chipenrich.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chipenrich/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chipenrich’ version ‘2.16.0’
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'hybridenrich':
hybridenrich
  Code: function(peaks, out_name = "hybridenrich", out_path = getwd(),
                 genome = supported_genomes(), genesets = c("GOBP",
                 "GOCC", "GOMF"), locusdef = "nearest_tss", methods =
                 c("chipenrich", "polyenrich"), weighting = NULL,
                 mappability = NULL, qc_plots = TRUE, min_geneset_size
                 = 15, max_geneset_size = 2000, num_peak_threshold = 1,
                 randomization = NULL, n_cores = 1)
  Docs: function(peaks, out_name = "hybridenrich", out_path = getwd(),
                 genome = supported_genomes(), genesets = c("GOBP",
                 "GOCC", "GOMF"), locusdef = "nearest_tss", methods =
                 c("chipenrich", "polyenrich"), weighting = NULL,
                 mappability = NULL, qc_plots = TRUE, min_geneset_size
                 = 15, max_geneset_size = 2000, num_peak_threshold = 1,
                 randomization = NULL, n_cores = 1, uuid = NULL)
  Argument names in docs not in code:
    uuid

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'hybridenrich'
  ‘uuid’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
polyenrich  6.447  0.787   7.236
broadenrich 6.031  0.099   6.136
* 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 WARNINGs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/chipenrich.Rcheck/00check.log’
for details.



Installation output

chipenrich.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL chipenrich
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
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(chipenrich)





> 
> test_check("chipenrich")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 170 ]
> 
> proc.time()
   user  system elapsed 
141.383   3.076 144.470 

Example timings

chipenrich.Rcheck/chipenrich-Ex.timings

nameusersystemelapsed
assign_peak_segments0.2790.0010.282
assign_peaks1.6730.0271.704
broadenrich6.0310.0996.136
calc_peak_gene_overlap0.3210.0000.322
chipenrich1.6530.0161.669
load_peaks0.0740.0000.075
num_peaks_per_gene0.4960.0200.516
peaks2genes0.5500.0030.553
plot_chipenrich_spline2.4330.0762.512
plot_dist_to_tss0.3800.0040.384
plot_gene_coverage0.8350.0000.835
plot_polyenrich_spline2.9550.0523.007
polyenrich6.4470.7877.236
proxReg0.5640.0580.623
read_bed0.3140.0120.327
supported_genesets0.0080.0000.007
supported_genomes0.0020.0000.002
supported_locusdefs0.0010.0080.009
supported_methods0.0010.0000.002
supported_read_lengths0.0030.0040.008