Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2021-11-29 15:05:36 -0500 (Mon, 29 Nov 2021).

CHECK results for regutools on tokay2

To the developers/maintainers of the regutools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/regutools.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 1576/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regutools 1.6.0  (landing page)
Joselyn Chavez
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/regutools
git_branch: RELEASE_3_14
git_last_commit: 3795415
git_last_commit_date: 2021-10-26 12:59:29 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: regutools
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regutools.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings regutools_1.6.0.tar.gz
StartedAt: 2021-11-29 03:40:29 -0500 (Mon, 29 Nov 2021)
EndedAt: 2021-11-29 03:56:48 -0500 (Mon, 29 Nov 2021)
EllapsedTime: 979.6 seconds
RetCode: 0
Status:   OK  
CheckDir: regutools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regutools.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings regutools_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/regutools.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 'regutools/DESCRIPTION' ... OK
* this is package 'regutools' version '1.6.0'
* 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       11.75   0.31   12.56
build_condition         9.58   1.19   11.60
convert_to_granges      8.74   0.64    9.71
convert_to_biostrings   7.83   1.34   11.90
get_dataset             7.64   1.13    9.19
get_binding_sites       7.79   0.78    9.11
get_regulatory_summary  7.84   0.34    8.57
connect_database        7.17   0.78    8.30
regulondb               7.22   0.72    8.33
get_regulatory_network  7.52   0.39    9.56
get_dna_objects         7.57   0.31    8.31
get_gene_synonyms       7.42   0.32    8.08
guess_id                7.23   0.34    7.97
list_datasets           6.98   0.38    7.72
list_attributes         7.05   0.30    7.68
get_gene_regulators     6.92   0.42    7.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
plot_dna_objects       11.93   0.33   12.67
build_condition         8.14   0.42    9.17
connect_database        7.75   0.41    8.52
get_dataset             7.79   0.34    8.47
guess_id                7.60   0.45    8.41
get_regulatory_summary  7.45   0.39    8.18
get_gene_regulators     7.50   0.30    8.17
convert_to_biostrings   7.46   0.28    8.10
get_gene_synonyms       7.31   0.38    8.04
get_dna_objects         7.43   0.25    8.02
list_attributes         7.22   0.39    7.95
convert_to_granges      6.97   0.42    7.77
list_datasets           6.97   0.34    7.66
regulondb               6.57   0.35    7.27
get_regulatory_network  6.42   0.47    8.46
get_binding_sites       6.53   0.23    7.12
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/regutools_1.6.0.tar.gz && rm -rf regutools.buildbin-libdir && mkdir regutools.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=regutools.buildbin-libdir regutools_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL regutools_1.6.0.zip && rm regutools_1.6.0.tar.gz regutools_1.6.0.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  494k  100  494k    0     0   786k      0 --:--:-- --:--:-- --:--:--  786k
100  494k  100  494k    0     0   786k      0 --:--:-- --:--:-- --:--:--  786k

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_1.6.0.zip
* DONE (regutools)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'regutools' successfully unpacked and MD5 sums checked

Tests output

regutools.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("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 
 135.90    9.17  153.40 

regutools.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("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 
 138.03    6.56  151.95 

Example timings

regutools.Rcheck/examples_i386/regutools-Ex.timings

nameusersystemelapsed
build_condition 9.58 1.1911.60
connect_database7.170.788.30
convert_to_biostrings 7.83 1.3411.90
convert_to_granges8.740.649.71
existing_intervals000
existing_partial_match000
get_binding_sites7.790.789.11
get_dataset7.641.139.19
get_dna_objects7.570.318.31
get_gene_regulators6.920.427.75
get_gene_synonyms7.420.328.08
get_regulatory_network7.520.399.56
get_regulatory_summary7.840.348.57
guess_id7.230.347.97
list_attributes7.050.307.68
list_datasets6.980.387.72
non_existing_intervals000
plot_dna_objects11.75 0.3112.56
regulondb7.220.728.33

regutools.Rcheck/examples_x64/regutools-Ex.timings

nameusersystemelapsed
build_condition8.140.429.17
connect_database7.750.418.52
convert_to_biostrings7.460.288.10
convert_to_granges6.970.427.77
existing_intervals000
existing_partial_match000
get_binding_sites6.530.237.12
get_dataset7.790.348.47
get_dna_objects7.430.258.02
get_gene_regulators7.500.308.17
get_gene_synonyms7.310.388.04
get_regulatory_network6.420.478.46
get_regulatory_summary7.450.398.18
guess_id7.600.458.41
list_attributes7.220.397.95
list_datasets6.970.347.66
non_existing_intervals000
plot_dna_objects11.93 0.3312.67
regulondb6.570.357.27