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This page was generated on 2025-08-11 12:10 -0400 (Mon, 11 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4532
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 1692/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCAS 1.35.0  (landing page)
Bora Uyar
Snapshot Date: 2025-08-10 13:45 -0400 (Sun, 10 Aug 2025)
git_url: https://git.bioconductor.org/packages/RCAS
git_branch: devel
git_last_commit: 2067192
git_last_commit_date: 2025-04-15 11:03:46 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for RCAS on lconway

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: 1.35.0
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_1.35.0.tar.gz
StartedAt: 2025-08-10 23:32:45 -0400 (Sun, 10 Aug 2025)
EndedAt: 2025-08-10 23:44:48 -0400 (Sun, 10 Aug 2025)
EllapsedTime: 722.9 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_1.35.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/RCAS.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.35.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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               60.602  0.620  53.352
getMotifSummaryTable            22.364  0.575  68.327
calculateCoverageProfileList    13.646  0.837  14.603
getFeatureBoundaryCoverageMulti 13.391  1.013  14.555
calculateCoverageProfile        12.131  0.476  12.700
findDifferentialMotifs          10.298  0.331   9.830
summarizeQueryRegions            8.760  0.351   9.196
summarizeQueryRegionsMulti       8.529  0.396  26.141
getTargetedGenesTable            8.416  0.447   9.001
getTxdbFeaturesFromGRanges       7.893  0.323   8.313
getFeatureBoundaryCoverageBin    5.343  0.284   5.664
createDB                         3.532  0.179  19.721
* 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/4.5-x86_64/Resources/library’
* installing *source* package ‘RCAS’ ...
** this is package ‘RCAS’ version ‘1.35.0’
** 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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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 9928 | SKIP 0 | PASS 48 ]

[ FAIL 0 | WARN 9928 | SKIP 0 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
107.844   3.997 112.848 

Example timings

RCAS.Rcheck/RCAS-Ex.timings

nameusersystemelapsed
calculateCoverageProfile12.131 0.47612.700
calculateCoverageProfileList13.646 0.83714.603
checkSeqDb0.3850.0390.493
createControlRegions0.2720.0040.278
createDB 3.532 0.17919.721
discoverFeatureSpecificMotifs0.0000.0000.001
extractSequences1.8670.2082.112
findDifferentialMotifs10.298 0.331 9.830
findEnrichedFunctions0.5790.0204.827
generateKmers0.0000.0010.001
getFeatureBoundaryCoverage4.4500.2364.730
getFeatureBoundaryCoverageBin5.3430.2845.664
getFeatureBoundaryCoverageMulti13.391 1.01314.555
getIntervalOverlapMatrix0.8910.0641.355
getMotifSummaryTable22.364 0.57568.327
getPWM0.0010.0010.002
getTargetedGenesTable8.4160.4479.001
getTxdbFeaturesFromGRanges7.8930.3238.313
importBed0.2510.0260.280
importBedFiles1.0700.1181.200
importGtf0.0010.0010.000
plotFeatureBoundaryCoverage4.4420.2084.688
queryGff1.6370.1171.773
runMotifDiscovery60.602 0.62053.352
runReport0.0010.0010.000
runReportMetaAnalysis1.1190.2781.706
summarizeQueryRegions8.7600.3519.196
summarizeQueryRegionsMulti 8.529 0.39626.141