Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:06 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

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 300/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chipenrich 2.18.0  (landing page)
Raymond G. Cavalcante
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/chipenrich
git_branch: RELEASE_3_14
git_last_commit: 3af75df
git_last_commit_date: 2021-10-26 12:09:44 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

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: 2022-01-20 17:24:51 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 17:37:10 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 738.5 seconds
RetCode: 0
Status:   OK  
CheckDir: chipenrich.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/chipenrich.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 8.43   0.26    8.83
polyenrich  7.92   0.01    7.94
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
broadenrich 7.86   0.16    8.02
polyenrich  7.51   0.02    7.53
* 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


Installation output

chipenrich.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


  % 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  115k  100  115k    0     0   603k      0 --:--:-- --:--:-- --:--:--  606k

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

Tests output

chipenrich.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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")
== Skipped tests ===============================================================
* empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 170 ]
> 
> proc.time()
   user  system elapsed 
 159.81    4.57  169.43 

chipenrich.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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")
== Skipped tests ===============================================================
* empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 170 ]
> 
> proc.time()
   user  system elapsed 
 152.93    2.75  155.65 

Example timings

chipenrich.Rcheck/examples_i386/chipenrich-Ex.timings

nameusersystemelapsed
assign_peak_segments0.480.030.65
assign_peaks1.750.051.91
broadenrich8.430.268.83
calc_peak_gene_overlap0.340.000.34
chipenrich1.720.001.75
load_peaks0.060.000.06
num_peaks_per_gene0.550.000.55
peaks2genes0.550.000.55
plot_chipenrich_spline2.710.112.92
plot_dist_to_tss0.350.000.34
plot_gene_coverage1.720.021.74
plot_polyenrich_spline2.090.052.14
polyenrich7.920.017.94
proxReg0.470.000.48
read_bed0.330.000.33
supported_genesets000
supported_genomes000
supported_locusdefs0.010.000.01
supported_methods000
supported_read_lengths000

chipenrich.Rcheck/examples_x64/chipenrich-Ex.timings

nameusersystemelapsed
assign_peak_segments0.230.010.25
assign_peaks0.740.000.73
broadenrich7.860.168.02
calc_peak_gene_overlap0.390.000.39
chipenrich2.990.013.00
load_peaks0.090.000.09
num_peaks_per_gene0.530.000.53
peaks2genes0.580.000.58
plot_chipenrich_spline1.580.031.61
plot_dist_to_tss0.390.020.40
plot_gene_coverage1.530.001.54
plot_polyenrich_spline2.880.143.01
polyenrich7.510.027.53
proxReg0.520.000.52
read_bed0.310.000.31
supported_genesets000
supported_genomes000
supported_locusdefs000
supported_methods000
supported_read_lengths0.000.010.01