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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1679/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCAS 1.32.0  (landing page)
Bora Uyar
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/RCAS
git_branch: RELEASE_3_20
git_last_commit: 6e3cea1
git_last_commit_date: 2024-10-29 10:12:38 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 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 RCAS on merida1

To the developers/maintainers of the RCAS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCAS.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: RCAS
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCAS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCAS_1.32.0.tar.gz
StartedAt: 2024-12-20 08:14:52 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 08:35:55 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 1263.2 seconds
RetCode: 0
Status:   OK  
CheckDir: RCAS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCAS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCAS_1.32.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RCAS.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCAS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCAS’ version ‘1.32.0’
* 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 ‘RCAS’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
runMotifDiscovery               84.388  0.731  77.690
getFeatureBoundaryCoverageMulti 27.211  2.172  29.741
getMotifSummaryTable            28.596  0.655 108.747
calculateCoverageProfileList    24.257  1.316  25.714
calculateCoverageProfile        18.874  0.792  19.971
findDifferentialMotifs          19.205  0.382  17.284
summarizeQueryRegions           16.812  0.533  17.711
getTargetedGenesTable           15.765  0.441  16.169
getTxdbFeaturesFromGRanges      15.587  0.459  16.432
summarizeQueryRegionsMulti      15.290  0.475  45.813
getFeatureBoundaryCoverageBin    8.918  0.345   9.322
plotFeatureBoundaryCoverage      8.468  0.168   8.681
getFeatureBoundaryCoverage       7.932  0.204   8.168
createDB                         6.766  0.191  35.994
* 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

RCAS.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RCAS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘RCAS’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package keeps a record of temporary installation path
* DONE (RCAS)

Tests output

RCAS.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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(RCAS)
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Loading required package: DT
Loading required package: data.table
Warning message:
replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' 
> 
> test_check("RCAS")
[ FAIL 0 | WARN 9938 | SKIP 0 | PASS 48 ]

[ FAIL 0 | WARN 9938 | SKIP 0 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
212.355   5.389 230.159 

Example timings

RCAS.Rcheck/RCAS-Ex.timings

nameusersystemelapsed
calculateCoverageProfile18.874 0.79219.971
calculateCoverageProfileList24.257 1.31625.714
checkSeqDb0.5270.0460.749
createControlRegions0.6940.0460.743
createDB 6.766 0.19135.994
discoverFeatureSpecificMotifs0.0010.0010.001
extractSequences3.3520.3203.803
findDifferentialMotifs19.205 0.38217.284
findEnrichedFunctions0.9920.0153.713
generateKmers0.0010.0010.001
getFeatureBoundaryCoverage7.9320.2048.168
getFeatureBoundaryCoverageBin8.9180.3459.322
getFeatureBoundaryCoverageMulti27.211 2.17229.741
getIntervalOverlapMatrix1.9040.0722.495
getMotifSummaryTable 28.596 0.655108.747
getPWM0.0010.0020.004
getTargetedGenesTable15.765 0.44116.169
getTxdbFeaturesFromGRanges15.587 0.45916.432
importBed0.5370.0310.569
importBedFiles2.2110.1292.346
importGtf0.0000.0010.001
plotFeatureBoundaryCoverage8.4680.1688.681
queryGff1.0510.0711.392
runMotifDiscovery84.388 0.73177.690
runReport0.0000.0020.001
runReportMetaAnalysis1.9300.3752.554
summarizeQueryRegions16.812 0.53317.711
summarizeQueryRegionsMulti15.290 0.47545.813