Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:10 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1644/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCAS 1.26.0  (landing page)
Bora Uyar
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/RCAS
git_branch: RELEASE_3_17
git_last_commit: 64293a9
git_last_commit_date: 2023-04-25 10:48:24 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for RCAS on kjohnson2


To the developers/maintainers of the RCAS package:
- 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: 1.26.0
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_1.26.0.tar.gz
StartedAt: 2023-10-18 17:28:52 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 17:44:54 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 961.6 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_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/RCAS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCAS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCAS’ version ‘1.26.0’
* 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 R 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               61.281  0.861  71.839
getMotifSummaryTable            24.889  0.933 106.833
getFeatureBoundaryCoverageMulti 16.296  0.818  26.319
calculateCoverageProfileList    13.598  0.345  21.157
findDifferentialMotifs          13.138  0.361  17.061
calculateCoverageProfile        11.459  0.315  17.908
summarizeQueryRegionsMulti      10.028  0.287  39.380
summarizeQueryRegions            9.583  0.262  14.959
getTxdbFeaturesFromGRanges       9.270  0.467  13.986
getTargetedGenesTable            9.162  0.540  14.553
getFeatureBoundaryCoverage       5.424  0.287   8.867
plotFeatureBoundaryCoverage      4.971  0.112   5.593
getFeatureBoundaryCoverageBin    4.812  0.132   7.770
createDB                         3.867  0.249  31.139
runReportMetaAnalysis            1.142  0.531   5.549
checkSeqDb                       0.391  0.037   7.475
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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 11 | SKIP 0 | PASS 48 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
 44.256   1.940  69.033 

Example timings

RCAS.Rcheck/RCAS-Ex.timings

nameusersystemelapsed
calculateCoverageProfile11.459 0.31517.908
calculateCoverageProfileList13.598 0.34521.157
checkSeqDb0.3910.0377.475
createControlRegions0.3010.0080.468
createDB 3.867 0.24931.139
discoverFeatureSpecificMotifs000
extractSequences1.9540.4284.051
findDifferentialMotifs13.138 0.36117.061
findEnrichedFunctions0.6990.0394.259
generateKmers0.0010.0000.001
getFeatureBoundaryCoverage5.4240.2878.867
getFeatureBoundaryCoverageBin4.8120.1327.770
getFeatureBoundaryCoverageMulti16.296 0.81826.319
getIntervalOverlapMatrix1.1700.0822.623
getMotifSummaryTable 24.889 0.933106.833
getTargetedGenesTable 9.162 0.54014.553
getTxdbFeaturesFromGRanges 9.270 0.46713.986
importBed0.2840.0220.360
importBedFiles1.1840.0831.481
importGtf000
plotFeatureBoundaryCoverage4.9710.1125.593
queryGff0.6300.0160.884
runMotifDiscovery61.281 0.86171.839
runReport0.0000.0000.001
runReportMetaAnalysis1.1420.5315.549
summarizeQueryRegions 9.583 0.26214.959
summarizeQueryRegionsMulti10.028 0.28739.380