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This page was generated on 2024-05-13 11:32:11 -0400 (Mon, 13 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4378
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Package 1679/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regutools 1.17.0  (landing page)
Joselyn Chavez
Snapshot Date: 2024-05-11 09:00:03 -0400 (Sat, 11 May 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)
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:
- 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: 2024-05-13 00:19:28 -0400 (Mon, 13 May 2024)
EndedAt: 2024-05-13 00:29:31 -0400 (Mon, 13 May 2024)
EllapsedTime: 603.2 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-mac-arm64/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       11.242  0.468  12.356
convert_to_biostrings   6.749  0.334   7.755
build_condition         5.758  0.326   7.122
get_dataset             5.274  0.353   6.568
get_regulatory_summary  5.190  0.330   6.436
convert_to_granges      5.234  0.275   6.410
get_dna_objects         5.042  0.363   6.297
get_regulatory_network  5.136  0.268   6.063
connect_database        5.015  0.354   6.018
get_gene_regulators     4.960  0.345   5.957
get_gene_synonyms       4.950  0.319   5.919
get_binding_sites       5.005  0.241   5.887
list_attributes         4.909  0.336   5.891
regulondb               4.829  0.393   5.884
list_datasets           4.819  0.221   5.914
guess_id                4.472  0.286   5.441
* 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 
101.105   5.843 118.228 

Example timings

regutools.Rcheck/regutools-Ex.timings

nameusersystemelapsed
build_condition5.7580.3267.122
connect_database5.0150.3546.018
convert_to_biostrings6.7490.3347.755
convert_to_granges5.2340.2756.410
existing_intervals0.0000.0000.001
existing_partial_match0.0000.0000.001
get_binding_sites5.0050.2415.887
get_dataset5.2740.3536.568
get_dna_objects5.0420.3636.297
get_gene_regulators4.9600.3455.957
get_gene_synonyms4.9500.3195.919
get_regulatory_network5.1360.2686.063
get_regulatory_summary5.1900.3306.436
guess_id4.4720.2865.441
list_attributes4.9090.3365.891
list_datasets4.8190.2215.914
non_existing_intervals0.0010.0000.001
plot_dna_objects11.242 0.46812.356
regulondb4.8290.3935.884