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This page was generated on 2024-03-18 11:36:55 -0400 (Mon, 18 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-06 r86056) -- "Unsuffered Consequences" 4685
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-06 r86056 ucrt) -- "Unsuffered Consequences" 4423
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-04 r86048) -- "Unsuffered Consequences" 4450
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-06 r86056) -- "Unsuffered Consequences" 4361
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 1702/2257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regutools 1.15.0  (landing page)
Joselyn Chavez
Snapshot Date: 2024-03-17 14:00:14 -0400 (Sun, 17 Mar 2024)
git_url: https://git.bioconductor.org/packages/regutools
git_branch: devel
git_last_commit: 852059b
git_last_commit_date: 2023-10-24 11:22:02 -0400 (Tue, 24 Oct 2023)
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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for regutools on nebbiolo1


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: 1.15.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:regutools.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings regutools_1.15.0.tar.gz
StartedAt: 2024-03-18 01:46:59 -0400 (Mon, 18 Mar 2024)
EndedAt: 2024-03-18 01:55:50 -0400 (Mon, 18 Mar 2024)
EllapsedTime: 531.2 seconds
RetCode: 0
Status:   OK  
CheckDir: regutools.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:regutools.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings regutools_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/regutools.Rcheck’
* using R Under development (unstable) (2024-03-06 r86056)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘regutools/DESCRIPTION’ ... OK
* this is package ‘regutools’ version ‘1.15.0’
* 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 loading without being on the library search path ... 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 8.420  0.903   9.502
connect_database 4.582  0.900   5.687
build_condition  4.562  0.852   5.668
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

regutools.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL regutools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 Under development (unstable) (2024-03-06 r86056) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 2 | SKIP 0 | PASS 110 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 110 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 74.093  10.797  87.987 

Example timings

regutools.Rcheck/regutools-Ex.timings

nameusersystemelapsed
build_condition4.5620.8525.668
connect_database4.5820.9005.687
convert_to_biostrings3.6420.5734.514
convert_to_granges3.4440.5564.218
existing_intervals0.0000.0000.001
existing_partial_match0.0000.0000.001
get_binding_sites3.2340.5193.930
get_dataset3.5030.6154.337
get_dna_objects3.4000.4764.066
get_gene_regulators3.3680.4754.017
get_gene_synonyms3.3650.4934.032
get_regulatory_network3.2420.4773.895
get_regulatory_summary3.4860.4994.177
guess_id3.2180.4173.811
list_attributes3.1240.3913.696
list_datasets3.2150.5073.898
non_existing_intervals0.0010.0000.000
plot_dna_objects8.4200.9039.502
regulondb3.1100.6273.942