Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-27 11:11:26 -0500 (Thu, 27 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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 merida1


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? here 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 1573/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regutools 1.7.1  (landing page)
Joselyn Chavez
Snapshot Date: 2022-01-26 13:55:18 -0500 (Wed, 26 Jan 2022)
git_url: https://git.bioconductor.org/packages/regutools
git_branch: master
git_last_commit: c4d9394
git_last_commit_date: 2021-11-22 22:51:31 -0500 (Mon, 22 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'AnnotationDbi' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: regutools
Version: 1.7.1
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_1.7.1.tar.gz
StartedAt: 2022-01-27 04:58:03 -0500 (Thu, 27 Jan 2022)
EndedAt: 2022-01-27 05:10:19 -0500 (Thu, 27 Jan 2022)
EllapsedTime: 736.4 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_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/regutools.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘regutools/DESCRIPTION’ ... OK
* this is package ‘regutools’ version ‘1.7.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 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       13.714  0.308  14.320
build_condition         7.381  0.511   8.648
connect_database        6.962  0.299   7.629
get_regulatory_summary  6.706  0.235   7.825
convert_to_granges      6.422  0.364   7.113
convert_to_biostrings   6.283  0.383   7.039
get_dataset             6.221  0.306   6.753
guess_id                6.221  0.241   7.405
list_attributes         6.142  0.265   6.665
regulondb               6.044  0.342   6.606
list_datasets           6.021  0.265   6.564
get_gene_regulators     6.025  0.250   6.510
get_binding_sites       5.958  0.262   6.570
get_dna_objects         5.877  0.241   6.454
get_gene_synonyms       5.859  0.249   6.438
get_regulatory_network  5.808  0.230   6.274
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/regutools.Rcheck/00check.log’
for details.



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/4.2/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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
133.337   5.826 146.604 

Example timings

regutools.Rcheck/regutools-Ex.timings

nameusersystemelapsed
build_condition7.3810.5118.648
connect_database6.9620.2997.629
convert_to_biostrings6.2830.3837.039
convert_to_granges6.4220.3647.113
existing_intervals0.0010.0000.000
existing_partial_match0.0000.0000.001
get_binding_sites5.9580.2626.570
get_dataset6.2210.3066.753
get_dna_objects5.8770.2416.454
get_gene_regulators6.0250.2506.510
get_gene_synonyms5.8590.2496.438
get_regulatory_network5.8080.2306.274
get_regulatory_summary6.7060.2357.825
guess_id6.2210.2417.405
list_attributes6.1420.2656.665
list_datasets6.0210.2656.564
non_existing_intervals0.0000.0000.001
plot_dna_objects13.714 0.30814.320
regulondb6.0440.3426.606