Multiple platform build/check report for BioC 3.14 - CHECK results for chipenrich on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: chipenrich

Version: 2.18.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chipenrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings chipenrich_2.18.0.tar.gz

StartedAt: 2022-04-12 17:11:48 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 17:23:55 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 727.0 seconds

RetCode: 0

Status: OK

CheckDir: chipenrich.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chipenrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings chipenrich_2.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/chipenrich.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '2.18.0'
* 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 ... OK
* checking Rd \usage sections ... OK
* 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 7.46   0.25    7.73
polyenrich  5.75   0.00    5.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
broadenrich 7.68   0.05    7.74
polyenrich  7.62   0.03    7.66
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/chipenrich_2.18.0.tar.gz && rm -rf chipenrich.buildbin-libdir && mkdir chipenrich.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chipenrich.buildbin-libdir chipenrich_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL chipenrich_2.18.0.zip && rm chipenrich_2.18.0.tar.gz chipenrich_2.18.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 43  115k   43 51111    0     0   260k      0 --:--:-- --:--:-- --:--:--  261k
100  115k  100  115k    0     0   186k      0 --:--:-- --:--:-- --:--:--  186k

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_2.18.0.zip
* DONE (chipenrich)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'chipenrich' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 3 | PASS 170 ]

== Skipped tests ===============================================================
* empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 170 ]
> 
> proc.time()
   user  system elapsed 
 143.85    4.26  154.59


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 3 | PASS 170 ]

== Skipped tests ===============================================================
* empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 170 ]
> 
> proc.time()
   user  system elapsed 
 168.84    2.56  171.39

name	user	system	elapsed
assign_peak_segments	0.33	0.00	0.40
assign_peaks	1.60	0.08	1.70
broadenrich	7.46	0.25	7.73
calc_peak_gene_overlap	0.34	0.03	0.38
chipenrich	2.58	0.00	2.59
load_peaks	0.09	0.00	0.09
num_peaks_per_gene	0.47	0.00	0.47
peaks2genes	0.55	0.01	0.57
plot_chipenrich_spline	2.50	0.07	2.67
plot_dist_to_tss	0.31	0.00	0.31
plot_gene_coverage	0.80	0.03	0.83
plot_polyenrich_spline	3.40	0.17	3.58
polyenrich	5.75	0.00	5.75
proxReg	0.46	0.01	0.47
read_bed	0.28	0.00	0.28
supported_genesets	0	0	0
supported_genomes	0	0	0
supported_locusdefs	0.01	0.00	0.01
supported_methods	0	0	0
supported_read_lengths	0	0	0

name	user	system	elapsed
assign_peak_segments	0.31	0.03	0.34
assign_peaks	0.61	0.01	0.63
broadenrich	7.68	0.05	7.74
calc_peak_gene_overlap	0.35	0.00	0.34
chipenrich	1.65	0.00	1.66
load_peaks	0.07	0.00	0.06
num_peaks_per_gene	0.45	0.01	0.47
peaks2genes	0.75	0.02	0.76
plot_chipenrich_spline	1.58	0.01	1.59
plot_dist_to_tss	0.34	0.02	0.36
plot_gene_coverage	1.66	0.00	1.66
plot_polyenrich_spline	2.78	0.11	2.89
polyenrich	7.62	0.03	7.66
proxReg	0.49	0.00	0.48
read_bed	0.33	0.00	0.33
supported_genesets	0	0	0
supported_genomes	0.01	0.00	0.02
supported_locusdefs	0	0	0
supported_methods	0	0	0
supported_read_lengths	0.02	0.00	0.01

CHECK results for chipenrich on tokay2

Summary

Command output

Installation output

Tests output

Example timings