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

This page was generated on 2021-12-01 17:18:30 -0500 (Wed, 01 Dec 2021).

CHECK results for regutools on machv2

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: 2021-11-30 04:15:05 -0500 (Tue, 30 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:regutools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings regutools_1.6.0.tar.gz
StartedAt: 2021-11-30 20:31:22 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 20:42:39 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 677.1 seconds
RetCode: 0
Status:   OK  
CheckDir: regutools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:regutools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings regutools_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/regutools.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
plot_dna_objects       13.131  0.341  13.997
build_condition         9.511  0.477  10.949
connect_database        8.629  0.401   9.685
get_regulatory_summary  7.794  0.343   8.636
convert_to_biostrings   7.522  0.414   8.535
convert_to_granges      7.416  0.340   8.286
guess_id                7.092  0.317   7.878
get_dataset             6.960  0.327   7.736
get_dna_objects         6.886  0.291   7.770
get_binding_sites       6.645  0.271   7.333
list_attributes         6.683  0.233   7.369
get_gene_synonyms       6.528  0.242   7.206
list_datasets           6.483  0.248   7.245
get_regulatory_network  6.371  0.253   7.045
get_gene_regulators     6.316  0.241   7.025
regulondb               6.218  0.274   6.911
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL regutools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘regutools’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** 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
* DONE (regutools)

Tests output

regutools.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
131.977   5.372 148.419 

Example timings

regutools.Rcheck/regutools-Ex.timings

nameusersystemelapsed
build_condition 9.511 0.47710.949
connect_database8.6290.4019.685
convert_to_biostrings7.5220.4148.535
convert_to_granges7.4160.3408.286
existing_intervals0.0010.0000.001
existing_partial_match0.0000.0010.001
get_binding_sites6.6450.2717.333
get_dataset6.9600.3277.736
get_dna_objects6.8860.2917.770
get_gene_regulators6.3160.2417.025
get_gene_synonyms6.5280.2427.206
get_regulatory_network6.3710.2537.045
get_regulatory_summary7.7940.3438.636
guess_id7.0920.3177.878
list_attributes6.6830.2337.369
list_datasets6.4830.2487.245
non_existing_intervals000
plot_dna_objects13.131 0.34113.997
regulondb6.2180.2746.911