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This page was generated on 2021-09-24 15:06:05 -0400 (Fri, 24 Sep 2021).

CHECK results for chipenrich on tokay2

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.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 292/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chipenrich 2.16.0  (landing page)
Raymond G. Cavalcante
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chipenrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings chipenrich_2.16.0.tar.gz
StartedAt: 2021-09-23 20:18:39 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 20:30:26 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 707.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: chipenrich.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chipenrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings chipenrich_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/chipenrich.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
broadenrich 7.35   0.20    7.63
polyenrich  7.03   0.16    7.19
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
broadenrich 7.62   0.10    7.72
polyenrich  6.54   0.02    6.56
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/chipenrich.Rcheck/00check.log'
for details.



Installation output

chipenrich.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/chipenrich_2.16.0.tar.gz && rm -rf chipenrich.buildbin-libdir && mkdir chipenrich.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chipenrich.buildbin-libdir chipenrich_2.16.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL chipenrich_2.16.0.zip && rm chipenrich_2.16.0.tar.gz chipenrich_2.16.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  2  115k    2  2487    0     0  25765      0  0:00:04 --:--:--  0:00:04 25639
100  115k  100  115k    0     0   562k      0 --:--:-- --:--:-- --:--:--  562k

install for i386

* installing *source* package 'chipenrich' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'chipenrich'
    finding HTML links ... done
    assign_peak_segments                    html  
    assign_peaks                            html  
    broadenrich                             html  
    calc_peak_gene_overlap                  html  
    chipenrich                              html  
    chipenrich_package                      html  
    filter_genesets                         html  
    genome_to_organism                      html  
    genome_to_orgdb                         html  
    get_test_method                         html  
    hybridenrich                            html  
    load_peaks                              html  
    num_peaks_per_gene                      html  
    peaks2genes                             html  
    plot_chipenrich_spline                  html  
    plot_dist_to_tss                        html  
    plot_gene_coverage                      html  
    plot_polyenrich_spline                  html  
    polyenrich                              html  
    post_process_enrichments                html  
    postprocess_peak_grs                    html  
    proxReg                                 html  
    read_bed                                html  
    read_geneset                            html  
    read_ldef                               html  
    read_mappa                              html  
    recode_peaks                            html  
    reset_ncores_for_windows                html  
    setup_genesets                          html  
    setup_locusdef                          html  
    setup_mappa                             html  
    supported_genesets                      html  
    supported_genomes                       html  
    supported_locusdefs                     html  
    supported_methods                       html  
    supported_read_lengths                  html  
** 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

install for x64

* installing *source* package 'chipenrich' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chipenrich' as chipenrich_2.16.0.zip
* DONE (chipenrich)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'chipenrich' successfully unpacked and MD5 sums checked

Tests output

chipenrich.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
 160.62    4.46  173.87 

chipenrich.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
 152.65    2.71  155.39 

Example timings

chipenrich.Rcheck/examples_i386/chipenrich-Ex.timings

nameusersystemelapsed
assign_peak_segments0.450.000.52
assign_peaks0.890.000.92
broadenrich7.350.207.63
calc_peak_gene_overlap0.310.000.31
chipenrich1.590.021.64
load_peaks0.080.000.08
num_peaks_per_gene0.490.010.50
peaks2genes0.500.020.51
plot_chipenrich_spline2.480.062.66
plot_dist_to_tss0.340.000.34
plot_gene_coverage0.770.030.80
plot_polyenrich_spline3.220.033.25
polyenrich7.030.167.19
proxReg0.480.000.50
read_bed0.290.000.28
supported_genesets0.010.000.01
supported_genomes000
supported_locusdefs000
supported_methods000
supported_read_lengths000

chipenrich.Rcheck/examples_x64/chipenrich-Ex.timings

nameusersystemelapsed
assign_peak_segments0.300.040.32
assign_peaks0.620.010.64
broadenrich7.620.107.72
calc_peak_gene_overlap0.310.010.32
chipenrich2.580.022.59
load_peaks0.080.000.08
num_peaks_per_gene0.560.010.58
peaks2genes0.540.000.55
plot_chipenrich_spline1.550.031.57
plot_dist_to_tss0.390.000.39
plot_gene_coverage0.860.020.88
plot_polyenrich_spline2.770.012.78
polyenrich6.540.026.56
proxReg0.390.000.39
read_bed0.250.000.25
supported_genesets000
supported_genomes000
supported_locusdefs0.000.020.02
supported_methods000
supported_read_lengths000