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This page was generated on 2025-09-20 12:03 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 1704/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCAS 1.35.0  (landing page)
Bora Uyar
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 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 24.04.3 LTS) / x86_64  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 13.7.7 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RCAS.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RCAS_1.35.0.tar.gz
StartedAt: 2025-09-20 03:21:52 -0400 (Sat, 20 Sep 2025)
EndedAt: 2025-09-20 03:34:26 -0400 (Sat, 20 Sep 2025)
EllapsedTime: 754.0 seconds
RetCode: 0
Status:   OK  
CheckDir: RCAS.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RCAS.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RCAS_1.35.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RCAS.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 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 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               50.801  1.361  45.312
getMotifSummaryTable            16.284  0.468  59.540
calculateCoverageProfileList    11.448  0.275  11.724
getFeatureBoundaryCoverageMulti 11.125  0.575  11.701
calculateCoverageProfile         9.605  0.457  10.062
findDifferentialMotifs           7.441  0.431   7.286
summarizeQueryRegionsMulti       6.911  0.327  23.068
getTargetedGenesTable            6.680  0.534   7.153
summarizeQueryRegions            6.681  0.311   6.993
getTxdbFeaturesFromGRanges       6.287  0.323   6.603
getFeatureBoundaryCoverageBin    4.693  0.415   5.110
createDB                         2.910  0.045  17.412
findEnrichedFunctions            0.645  0.184   6.372
* 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

RCAS.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL RCAS
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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(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 9947 | SKIP 0 | PASS 48 ]

[ FAIL 0 | WARN 9947 | SKIP 0 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
 88.122   4.284  92.045 

Example timings

RCAS.Rcheck/RCAS-Ex.timings

nameusersystemelapsed
calculateCoverageProfile 9.605 0.45710.062
calculateCoverageProfileList11.448 0.27511.724
checkSeqDb0.3380.0150.391
createControlRegions0.2310.0000.231
createDB 2.910 0.04517.412
discoverFeatureSpecificMotifs000
extractSequences1.3950.1811.577
findDifferentialMotifs7.4410.4317.286
findEnrichedFunctions0.6450.1846.372
generateKmers0.0000.0000.001
getFeatureBoundaryCoverage3.7580.5534.312
getFeatureBoundaryCoverageBin4.6930.4155.110
getFeatureBoundaryCoverageMulti11.125 0.57511.701
getIntervalOverlapMatrix2.0340.2112.506
getMotifSummaryTable16.284 0.46859.540
getPWM0.0010.0000.001
getTargetedGenesTable6.6800.5347.153
getTxdbFeaturesFromGRanges6.2870.3236.603
importBed0.2090.0130.224
importBedFiles0.8900.0840.976
importGtf0.0000.0000.001
plotFeatureBoundaryCoverage3.8440.1954.040
queryGff1.4980.2541.751
runMotifDiscovery50.801 1.36145.312
runReport0.0010.0000.000
runReportMetaAnalysis1.0300.1221.194
summarizeQueryRegions6.6810.3116.993
summarizeQueryRegionsMulti 6.911 0.32723.068