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CHECK report for chipenrich on tokay1

This page was generated on 2021-05-06 12:30:13 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the chipenrich package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 284/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chipenrich 2.14.0  (landing page)
Raymond G. Cavalcante
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/chipenrich
Branch: RELEASE_3_12
Last Commit: 2e41855
Last Changed Date: 2020-10-27 10:52:32 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
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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.



Installation output

chipenrich.Rcheck/00install.out

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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

Tests output

chipenrich.Rcheck/tests_i386/testthat.Rout


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 

chipenrich.Rcheck/tests_x64/testthat.Rout


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 

Example timings

chipenrich.Rcheck/examples_i386/chipenrich-Ex.timings

nameusersystemelapsed
assign_peak_segments0.330.001.30
assign_peaks0.780.021.03
broadenrich12.41 0.3912.92
calc_peak_gene_overlap0.620.010.64
chipenrich2.960.032.99
load_peaks0.090.000.09
num_peaks_per_gene0.940.020.95
peaks2genes0.980.011.00
plot_chipenrich_spline3.050.133.20
plot_dist_to_tss0.420.070.50
plot_gene_coverage1.450.041.49
plot_polyenrich_spline3.890.063.96
polyenrich9.530.089.61
proxReg0.700.000.77
read_bed0.30.00.3
supported_genesets000
supported_genomes0.010.000.01
supported_locusdefs000
supported_methods000
supported_read_lengths0.020.000.02

chipenrich.Rcheck/examples_x64/chipenrich-Ex.timings

nameusersystemelapsed
assign_peak_segments0.280.010.30
assign_peaks0.650.030.69
broadenrich8.140.168.30
calc_peak_gene_overlap0.440.000.44
chipenrich1.830.001.82
load_peaks0.070.000.08
num_peaks_per_gene0.60.00.6
peaks2genes0.560.020.57
plot_chipenrich_spline1.660.011.68
plot_dist_to_tss1.480.001.48
plot_gene_coverage0.880.000.88
plot_polyenrich_spline3.120.033.15
polyenrich8.310.028.33
proxReg0.480.000.48
read_bed0.280.000.28
supported_genesets000
supported_genomes000
supported_locusdefs0.020.000.02
supported_methods000
supported_read_lengths000