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This page was generated on 2024-12-23 11:41 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 1667/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCAS 1.33.0  (landing page)
Bora Uyar
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/RCAS
git_branch: devel
git_last_commit: 44fd977
git_last_commit_date: 2024-10-29 10:12:38 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for RCAS on nebbiolo1

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: 1.33.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RCAS.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RCAS_1.33.0.tar.gz
StartedAt: 2024-12-23 01:22:02 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 01:34:08 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 725.5 seconds
RetCode: 0
Status:   OK  
CheckDir: RCAS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RCAS.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RCAS_1.33.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RCAS.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘RCAS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCAS’ version ‘1.33.0’
* 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               46.496  0.665  41.496
getMotifSummaryTable            17.790  0.777  56.275
getFeatureBoundaryCoverageMulti 12.410  1.327  13.737
calculateCoverageProfileList    13.042  0.403  13.446
calculateCoverageProfile        10.816  0.381  11.201
findDifferentialMotifs           7.597  0.669   7.609
summarizeQueryRegionsMulti       7.757  0.449  23.205
getTxdbFeaturesFromGRanges       7.364  0.434   7.795
getTargetedGenesTable            6.770  0.483   7.211
summarizeQueryRegions            6.792  0.446   7.250
plotFeatureBoundaryCoverage      4.696  0.314   5.011
createDB                         3.023  0.248  17.505
* 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-3.21-bioc/R/bin/R CMD INSTALL RCAS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 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 9938 | SKIP 0 | PASS 48 ]

[ FAIL 0 | WARN 9938 | SKIP 0 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
 86.189   3.691  89.544 

Example timings

RCAS.Rcheck/RCAS-Ex.timings

nameusersystemelapsed
calculateCoverageProfile10.816 0.38111.201
calculateCoverageProfileList13.042 0.40313.446
checkSeqDb0.3480.0120.492
createControlRegions0.2510.0410.292
createDB 3.023 0.24817.505
discoverFeatureSpecificMotifs0.0010.0000.001
extractSequences1.4200.4441.864
findDifferentialMotifs7.5970.6697.609
findEnrichedFunctions0.5210.1344.817
generateKmers0.0000.0000.001
getFeatureBoundaryCoverage3.6860.4094.095
getFeatureBoundaryCoverageBin3.8850.3604.246
getFeatureBoundaryCoverageMulti12.410 1.32713.737
getIntervalOverlapMatrix0.8610.0731.186
getMotifSummaryTable17.790 0.77756.275
getPWM0.0010.0000.001
getTargetedGenesTable6.7700.4837.211
getTxdbFeaturesFromGRanges7.3640.4347.795
importBed0.2200.0210.242
importBedFiles0.9330.0510.985
importGtf000
plotFeatureBoundaryCoverage4.6960.3145.011
queryGff0.4130.0680.481
runMotifDiscovery46.496 0.66541.496
runReport000
runReportMetaAnalysis0.8370.1661.035
summarizeQueryRegions6.7920.4467.250
summarizeQueryRegionsMulti 7.757 0.44923.205