Multiple platform build/check report for BioC 3.12 - CHECK report for chipenrich on tokay1

Package: chipenrich

Version: 2.14.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chipenrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings chipenrich_2.14.0.tar.gz

StartedAt: 2021-05-06 01:21:23 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 01:35:40 -0400 (Thu, 06 May 2021)

EllapsedTime: 856.8 seconds

RetCode: 0

Status: OK

CheckDir: chipenrich.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chipenrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings chipenrich_2.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/chipenrich.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '2.14.0'
* 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 ... NOTE
proxReg: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
* 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 12.41   0.39   12.92
polyenrich   9.53   0.08    9.61
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
polyenrich  8.31   0.02    8.33
broadenrich 8.14   0.16    8.30
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/chipenrich.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/chipenrich_2.14.0.tar.gz && rm -rf chipenrich.buildbin-libdir && mkdir chipenrich.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chipenrich.buildbin-libdir chipenrich_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL chipenrich_2.14.0.zip && rm chipenrich_2.14.0.tar.gz chipenrich_2.14.0.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
100  114k  100  114k    0     0  7760k      0 --:--:-- --:--:-- --:--:-- 8157k

install for i386

* installing *source* package 'chipenrich' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** 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
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** testing if installed package can be loaded from final location
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** 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
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
* MD5 sums
packaged installation of 'chipenrich' as chipenrich_2.14.0.zip
* DONE (chipenrich)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'chipenrich' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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)





Warning message:
In .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
> 
> test_check("chipenrich")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 194 ]
> 
> proc.time()
   user  system elapsed 
 183.23    4.18  190.23


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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)





Warning message:
In .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
> 
> test_check("chipenrich")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 194 ]
> 
> proc.time()
   user  system elapsed 
 212.87    1.96  214.86

name	user	system	elapsed
assign_peak_segments	0.33	0.00	1.30
assign_peaks	0.78	0.02	1.03
broadenrich	12.41	0.39	12.92
calc_peak_gene_overlap	0.62	0.01	0.64
chipenrich	2.96	0.03	2.99
load_peaks	0.09	0.00	0.09
num_peaks_per_gene	0.94	0.02	0.95
peaks2genes	0.98	0.01	1.00
plot_chipenrich_spline	3.05	0.13	3.20
plot_dist_to_tss	0.42	0.07	0.50
plot_gene_coverage	1.45	0.04	1.49
plot_polyenrich_spline	3.89	0.06	3.96
polyenrich	9.53	0.08	9.61
proxReg	0.70	0.00	0.77
read_bed	0.3	0.0	0.3
supported_genesets	0	0	0
supported_genomes	0.01	0.00	0.01
supported_locusdefs	0	0	0
supported_methods	0	0	0
supported_read_lengths	0.02	0.00	0.02

name	user	system	elapsed
assign_peak_segments	0.28	0.01	0.30
assign_peaks	0.65	0.03	0.69
broadenrich	8.14	0.16	8.30
calc_peak_gene_overlap	0.44	0.00	0.44
chipenrich	1.83	0.00	1.82
load_peaks	0.07	0.00	0.08
num_peaks_per_gene	0.6	0.0	0.6
peaks2genes	0.56	0.02	0.57
plot_chipenrich_spline	1.66	0.01	1.68
plot_dist_to_tss	1.48	0.00	1.48
plot_gene_coverage	0.88	0.00	0.88
plot_polyenrich_spline	3.12	0.03	3.15
polyenrich	8.31	0.02	8.33
proxReg	0.48	0.00	0.48
read_bed	0.28	0.00	0.28
supported_genesets	0	0	0
supported_genomes	0	0	0
supported_locusdefs	0.02	0.00	0.02
supported_methods	0	0	0
supported_read_lengths	0	0	0

CHECK report for chipenrich on tokay1

Summary

Command output

Installation output

Tests output

Example timings