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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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

Package 1685/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regutools 1.17.0  (landing page)
Joselyn Chavez
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/regutools
git_branch: devel
git_last_commit: 0e8dd20
git_last_commit_date: 2024-04-30 11:23:44 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 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
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for regutools on kjohnson1

To the developers/maintainers of the regutools package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: regutools
Version: 1.17.0
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_1.17.0.tar.gz
StartedAt: 2024-06-11 05:49:26 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 05:59:35 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 609.1 seconds
RetCode: 0
Status:   OK  
CheckDir: regutools.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/regutools.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘regutools/DESCRIPTION’ ... OK
* this is package ‘regutools’ version ‘1.17.0’
* 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 code 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       11.160  0.420  12.317
convert_to_biostrings   6.689  0.391   8.010
build_condition         6.420  0.249   7.693
get_dataset             5.289  0.398   6.630
convert_to_granges      5.271  0.400   6.597
get_regulatory_summary  5.246  0.344   6.531
connect_database        5.032  0.369   6.059
get_dna_objects         5.020  0.319   5.992
get_gene_regulators     4.971  0.363   5.997
get_binding_sites       4.974  0.313   5.957
list_attributes         4.956  0.328   6.206
get_regulatory_network  4.977  0.265   6.146
guess_id                4.871  0.343   5.887
list_datasets           4.861  0.297   5.892
regulondb               4.848  0.302   5.815
get_gene_synonyms       4.655  0.312   5.666
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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/4.4-arm64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 
102.853   6.442 121.626 

Example timings

regutools.Rcheck/regutools-Ex.timings

nameusersystemelapsed
build_condition6.4200.2497.693
connect_database5.0320.3696.059
convert_to_biostrings6.6890.3918.010
convert_to_granges5.2710.4006.597
existing_intervals0.0010.0010.001
existing_partial_match0.0000.0000.001
get_binding_sites4.9740.3135.957
get_dataset5.2890.3986.630
get_dna_objects5.0200.3195.992
get_gene_regulators4.9710.3635.997
get_gene_synonyms4.6550.3125.666
get_regulatory_network4.9770.2656.146
get_regulatory_summary5.2460.3446.531
guess_id4.8710.3435.887
list_attributes4.9560.3286.206
list_datasets4.8610.2975.892
non_existing_intervals0.0010.0000.001
plot_dna_objects11.160 0.42012.317
regulondb4.8480.3025.815