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This page was generated on 2023-04-12 11:05:48 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 palomino4


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 1647/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regutools 1.10.0  (landing page)
Joselyn Chavez
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/regutools
git_branch: RELEASE_3_16
git_last_commit: 329ca37
git_last_commit_date: 2022-11-01 11:22:01 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: regutools
Version: 1.10.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:regutools.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings regutools_1.10.0.tar.gz
StartedAt: 2023-04-11 05:06:21 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 05:15:17 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 536.1 seconds
RetCode: 0
Status:   OK  
CheckDir: regutools.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:regutools.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings regutools_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/regutools.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'regutools/DESCRIPTION' ... OK
* this is package 'regutools' version '1.10.0'
* 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
* 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       10.76   0.41   11.20
build_condition         7.76   0.37    8.58
convert_to_granges      7.10   0.43    7.57
convert_to_biostrings   5.90   0.58    6.93
get_dataset             6.14   0.31    6.49
get_gene_regulators     5.96   0.40    6.46
regulondb               5.95   0.34    6.35
get_binding_sites       5.80   0.41    6.25
list_attributes         5.76   0.34    6.14
get_regulatory_summary  5.81   0.28    6.13
get_regulatory_network  5.68   0.40    8.17
guess_id                5.61   0.44    6.11
connect_database        5.55   0.49    6.06
get_dna_objects         5.66   0.35    6.18
get_gene_synonyms       5.61   0.35    5.98
list_datasets           5.43   0.39    5.84
* 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

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL regutools
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 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 
 112.85    6.65  122.67 

Example timings

regutools.Rcheck/regutools-Ex.timings

nameusersystemelapsed
build_condition7.760.378.58
connect_database5.550.496.06
convert_to_biostrings5.900.586.93
convert_to_granges7.100.437.57
existing_intervals000
existing_partial_match000
get_binding_sites5.800.416.25
get_dataset6.140.316.49
get_dna_objects5.660.356.18
get_gene_regulators5.960.406.46
get_gene_synonyms5.610.355.98
get_regulatory_network5.680.408.17
get_regulatory_summary5.810.286.13
guess_id5.610.446.11
list_attributes5.760.346.14
list_datasets5.430.395.84
non_existing_intervals000
plot_dna_objects10.76 0.4111.20
regulondb5.950.346.35