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This page was generated on 2024-06-11 14:44 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 1735/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regutools 1.16.0  (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: RELEASE_3_19
git_last_commit: 6c3f2fd
git_last_commit_date: 2024-04-30 11:23:44 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for regutools on kjohnson3

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: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2024-06-11 02:49:48 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 03:03:39 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 831.5 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/regutools.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘regutools/DESCRIPTION’ ... OK
* this is package ‘regutools’ version ‘1.16.0’
* 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       11.688  0.423  17.924
convert_to_biostrings   6.217  0.393  10.647
build_condition         5.485  0.343   9.303
get_dataset             4.289  0.348   7.662
get_regulatory_summary  4.281  0.309   7.197
get_regulatory_network  4.276  0.289   7.241
get_dna_objects         4.163  0.300   8.568
get_gene_synonyms       4.124  0.326   6.363
convert_to_granges      4.085  0.337   6.669
get_binding_sites       4.087  0.322   7.056
list_datasets           4.092  0.317   6.918
get_gene_regulators     4.088  0.317   8.276
connect_database        4.053  0.302   7.552
guess_id                4.015  0.309   5.675
list_attributes         3.997  0.284   5.524
regulondb               3.666  0.330   6.434
* 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 (2024-04-24) -- "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 
 89.062   6.191 129.007 

Example timings

regutools.Rcheck/regutools-Ex.timings

nameusersystemelapsed
build_condition5.4850.3439.303
connect_database4.0530.3027.552
convert_to_biostrings 6.217 0.39310.647
convert_to_granges4.0850.3376.669
existing_intervals0.0010.0000.001
existing_partial_match0.0000.0000.001
get_binding_sites4.0870.3227.056
get_dataset4.2890.3487.662
get_dna_objects4.1630.3008.568
get_gene_regulators4.0880.3178.276
get_gene_synonyms4.1240.3266.363
get_regulatory_network4.2760.2897.241
get_regulatory_summary4.2810.3097.197
guess_id4.0150.3095.675
list_attributes3.9970.2845.524
list_datasets4.0920.3176.918
non_existing_intervals0.0000.0010.001
plot_dna_objects11.688 0.42317.924
regulondb3.6660.3306.434