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CHECK report for regutools on tokay1

This page was generated on 2021-05-06 12:33:11 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the regutools package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1500/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regutools 1.2.3  (landing page)
Joselyn Chavez
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/regutools
Branch: RELEASE_3_12
Last Commit: 4c29caf
Last Changed Date: 2020-12-18 19:17:39 -0400 (Fri, 18 Dec 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: regutools
Version: 1.2.3
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regutools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings regutools_1.2.3.tar.gz
StartedAt: 2021-05-06 06:05:23 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:23:33 -0400 (Thu, 06 May 2021)
EllapsedTime: 1090.1 seconds
RetCode: 0
Status:   OK   
CheckDir: regutools.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:regutools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings regutools_1.2.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/regutools.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 'regutools/DESCRIPTION' ... OK
* this is package 'regutools' version '1.2.3'
* package encoding: UTF-8
* 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 'regutools' 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
plot_dna_objects       14.41   0.34   15.06
regulondb              10.28   1.24   11.77
list_datasets          10.79   0.39   11.44
guess_id                9.14   1.20   10.62
list_attributes         9.38   0.94   10.55
get_dna_objects         9.40   0.83   11.64
get_regulatory_network  9.31   0.61   12.38
get_gene_synonyms       9.02   0.65    9.90
get_binding_sites       9.04   0.34    9.81
build_condition         7.79   1.16    9.73
convert_to_biostrings   8.15   0.78   16.36
get_regulatory_summary  8.17   0.49    8.92
connect_database        7.98   0.31    8.53
get_gene_regulators     7.47   0.77    8.71
get_dataset             7.32   0.36    7.92
convert_to_granges      7.11   0.33    7.70
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
plot_dna_objects       11.16   0.22   11.61
convert_to_granges      7.91   0.36    8.50
build_condition         7.48   0.34    8.19
get_dna_objects         7.50   0.24    7.94
guess_id                7.03   0.36    7.61
convert_to_biostrings   6.91   0.36    7.51
connect_database        6.83   0.33    7.37
regulondb               6.83   0.23    7.40
get_binding_sites       6.77   0.20    7.61
get_regulatory_summary  6.67   0.27    7.15
get_dataset             6.59   0.25    7.06
get_gene_synonyms       6.46   0.27    6.95
get_regulatory_network  6.38   0.26    8.10
list_attributes         6.33   0.31    6.85
get_gene_regulators     6.24   0.34    6.81
list_datasets           6.34   0.17    6.83
* 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

regutools.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/regutools_1.2.3.tar.gz && rm -rf regutools.buildbin-libdir && mkdir regutools.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=regutools.buildbin-libdir regutools_1.2.3.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL regutools_1.2.3.zip && rm regutools_1.2.3.tar.gz regutools_1.2.3.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  493k  100  493k    0     0  4205k      0 --:--:-- --:--:-- --:--:-- 4258k

install for i386

* installing *source* package 'regutools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'regutools'
    finding HTML links ... done
    build_condition                         html  
    connect_database                        html  
    convert_to_biostrings                   html  
    convert_to_granges                      html  
    existing_intervals                      html  
    existing_partial_match                  html  
    get_binding_sites                       html  
    get_dataset                             html  
    get_dna_objects                         html  
    get_gene_regulators                     html  
    get_gene_synonyms                       html  
    get_regulatory_network                  html  
    get_regulatory_summary                  html  
    guess_id                                html  
    list_attributes                         html  
    list_datasets                           html  
    non_existing_intervals                  html  
    plot_dna_objects                        html  
    regulondb-class                         html  
    regulondb-methods                       html  
    regulondb                               html  
    regulondb_result-class                  html  
    regutools-package                       html  
*** copying figures
** 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 'regutools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'regutools' as regutools_1.2.3.zip
* DONE (regutools)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'regutools' successfully unpacked and MD5 sums checked

Tests output

regutools.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("regutools")
> 
> test_check("regutools")

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 110 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 146.18    8.98  165.04 

regutools.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("regutools")
> 
> test_check("regutools")

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 110 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 148.75    5.89  161.32 

Example timings

regutools.Rcheck/examples_i386/regutools-Ex.timings

nameusersystemelapsed
build_condition7.791.169.73
connect_database7.980.318.53
convert_to_biostrings 8.15 0.7816.36
convert_to_granges7.110.337.70
existing_intervals000
existing_partial_match000
get_binding_sites9.040.349.81
get_dataset7.320.367.92
get_dna_objects 9.40 0.8311.64
get_gene_regulators7.470.778.71
get_gene_synonyms9.020.659.90
get_regulatory_network 9.31 0.6112.38
get_regulatory_summary8.170.498.92
guess_id 9.14 1.2010.62
list_attributes 9.38 0.9410.55
list_datasets10.79 0.3911.44
non_existing_intervals000
plot_dna_objects14.41 0.3415.06
regulondb10.28 1.2411.77

regutools.Rcheck/examples_x64/regutools-Ex.timings

nameusersystemelapsed
build_condition7.480.348.19
connect_database6.830.337.37
convert_to_biostrings6.910.367.51
convert_to_granges7.910.368.50
existing_intervals000
existing_partial_match000
get_binding_sites6.770.207.61
get_dataset6.590.257.06
get_dna_objects7.500.247.94
get_gene_regulators6.240.346.81
get_gene_synonyms6.460.276.95
get_regulatory_network6.380.268.10
get_regulatory_summary6.670.277.15
guess_id7.030.367.61
list_attributes6.330.316.85
list_datasets6.340.176.83
non_existing_intervals000
plot_dna_objects11.16 0.2211.61
regulondb6.830.237.40