Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:12 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 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? 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: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
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 -0400 (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: 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: 2022-04-13 01:28:27 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 01:45:28 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 1020.7 seconds
RetCode: 0
Status:   OK  
CheckDir: regutools.Rcheck
Warnings: 0

Command output

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###
### 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 4.1.3 (2022-03-10)
* 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       12.80   0.48   13.67
build_condition        10.59   1.50   13.11
get_dna_objects        10.47   0.33   11.36
connect_database        7.99   1.68   10.05
convert_to_biostrings   8.60   1.00   14.73
get_gene_synonyms       8.94   0.40    9.69
regulondb               8.22   1.06    9.64
get_binding_sites       8.48   0.43    9.56
get_dataset             8.22   0.62    9.25
convert_to_granges      8.23   0.53    9.16
get_regulatory_network  8.29   0.30   10.17
guess_id                7.94   0.61    8.93
list_attributes         7.80   0.71    8.86
list_datasets           7.92   0.53    8.83
get_regulatory_summary  7.89   0.42    8.69
get_gene_regulators     7.66   0.36    8.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
plot_dna_objects       12.81   0.37   13.57
build_condition         9.22   0.40   10.28
connect_database        9.14   0.35    9.88
convert_to_biostrings   8.21   0.45    9.02
get_regulatory_summary  8.33   0.31    8.98
get_dataset             8.04   0.45    8.84
get_binding_sites       7.90   0.54    8.79
convert_to_granges      7.99   0.45    8.83
list_datasets           8.03   0.41    8.83
get_gene_synonyms       7.98   0.31    8.68
guess_id                7.86   0.36    8.59
list_attributes         7.87   0.23    8.49
regulondb               7.68   0.38    8.41
get_dna_objects         7.77   0.25    8.39
get_gene_regulators     7.58   0.39    8.34
get_regulatory_network  7.44   0.38    9.39
* 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
  3  494k    3 16011    0     0   133k      0  0:00:03 --:--:--  0:00:03  132k
100  494k  100  494k    0     0   657k      0 --:--:-- --:--:-- --:--:--  657k

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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
 149.20    9.71  166.87 

regutools.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
 144.64    7.12  159.26 

Example timings

regutools.Rcheck/examples_i386/regutools-Ex.timings

nameusersystemelapsed
build_condition10.59 1.5013.11
connect_database 7.99 1.6810.05
convert_to_biostrings 8.60 1.0014.73
convert_to_granges8.230.539.16
existing_intervals000
existing_partial_match000
get_binding_sites8.480.439.56
get_dataset8.220.629.25
get_dna_objects10.47 0.3311.36
get_gene_regulators7.660.368.53
get_gene_synonyms8.940.409.69
get_regulatory_network 8.29 0.3010.17
get_regulatory_summary7.890.428.69
guess_id7.940.618.93
list_attributes7.800.718.86
list_datasets7.920.538.83
non_existing_intervals000
plot_dna_objects12.80 0.4813.67
regulondb8.221.069.64

regutools.Rcheck/examples_x64/regutools-Ex.timings

nameusersystemelapsed
build_condition 9.22 0.4010.28
connect_database9.140.359.88
convert_to_biostrings8.210.459.02
convert_to_granges7.990.458.83
existing_intervals000
existing_partial_match000
get_binding_sites7.900.548.79
get_dataset8.040.458.84
get_dna_objects7.770.258.39
get_gene_regulators7.580.398.34
get_gene_synonyms7.980.318.68
get_regulatory_network7.440.389.39
get_regulatory_summary8.330.318.98
guess_id7.860.368.59
list_attributes7.870.238.49
list_datasets8.030.418.83
non_existing_intervals000
plot_dna_objects12.81 0.3713.57
regulondb7.680.388.41