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This page was generated on 2025-08-30 12:09 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 1695/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCAS 1.35.0  (landing page)
Bora Uyar
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 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 24.04.3 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: RCAS
Version: 1.35.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:RCAS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RCAS_1.35.0.tar.gz
StartedAt: 2025-08-29 10:37:20 -0000 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 10:49:49 -0000 (Fri, 29 Aug 2025)
EllapsedTime: 749.0 seconds
RetCode: 0
Status:   OK  
CheckDir: RCAS.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:RCAS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RCAS_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RCAS.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 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               41.039  0.438  35.756
getFeatureBoundaryCoverageMulti 17.082  0.391  17.508
getMotifSummaryTable            17.191  0.182  60.396
calculateCoverageProfileList    14.250  0.208  14.495
calculateCoverageProfile        12.152  0.292  12.530
findDifferentialMotifs          11.074  0.416  10.329
summarizeQueryRegionsMulti      10.708  0.149  28.879
getTargetedGenesTable            9.035  0.329   9.379
summarizeQueryRegions            8.701  0.112   8.833
getTxdbFeaturesFromGRanges       8.175  0.191   8.385
getFeatureBoundaryCoverageBin    6.035  0.144   6.191
plotFeatureBoundaryCoverage      5.183  0.124   5.317
createDB                         4.069  0.056  22.731
* 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL RCAS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 9937 | SKIP 0 | PASS 48 ]

[ FAIL 0 | WARN 9937 | SKIP 0 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
127.937   1.990 129.435 

Example timings

RCAS.Rcheck/RCAS-Ex.timings

nameusersystemelapsed
calculateCoverageProfile12.152 0.29212.530
calculateCoverageProfileList14.250 0.20814.495
checkSeqDb0.3760.0070.397
createControlRegions0.3430.0040.348
createDB 4.069 0.05622.731
discoverFeatureSpecificMotifs000
extractSequences2.0360.1882.232
findDifferentialMotifs11.074 0.41610.329
findEnrichedFunctions0.6520.0444.296
generateKmers0.0000.0000.001
getFeatureBoundaryCoverage4.7700.2124.992
getFeatureBoundaryCoverageBin6.0350.1446.191
getFeatureBoundaryCoverageMulti17.082 0.39117.508
getIntervalOverlapMatrix1.0910.0241.421
getMotifSummaryTable17.191 0.18260.396
getPWM0.0010.0010.001
getTargetedGenesTable9.0350.3299.379
getTxdbFeaturesFromGRanges8.1750.1918.385
importBed0.3050.0040.310
importBedFiles1.2810.0321.316
importGtf000
plotFeatureBoundaryCoverage5.1830.1245.317
queryGff1.4760.0841.564
runMotifDiscovery41.039 0.43835.756
runReport000
runReportMetaAnalysis1.4600.0871.644
summarizeQueryRegions8.7010.1128.833
summarizeQueryRegionsMulti10.708 0.14928.879