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This page was generated on 2024-03-04 11:39:32 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 1291/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
monaLisa 1.9.0  (landing page)
Michael Stadler
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/monaLisa
git_branch: devel
git_last_commit: f0d6458
git_last_commit_date: 2023-11-01 05:14:49 -0500 (Wed, 01 Nov 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for monaLisa on merida1


To the developers/maintainers of the monaLisa package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/monaLisa.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: monaLisa
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:monaLisa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings monaLisa_1.9.0.tar.gz
StartedAt: 2024-03-02 07:06:31 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 07:19:27 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 776.1 seconds
RetCode: 0
Status:   OK  
CheckDir: monaLisa.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:monaLisa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings monaLisa_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/monaLisa.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘monaLisa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘monaLisa’ version ‘1.9.0’
* package encoding: UTF-8
* 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 ‘monaLisa’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
plotMotifHeatmaps 10.278  0.178  12.134
* 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

monaLisa.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL monaLisa
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘monaLisa’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (monaLisa)

Tests output

monaLisa.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 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(monaLisa)

> 
> test_check("monaLisa")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 537 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_Homer.R:116:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 537 ]
> 
> proc.time()
   user  system elapsed 
 98.921   7.852 124.115 

Example timings

monaLisa.Rcheck/monaLisa-Ex.timings

nameusersystemelapsed
annoSeqlogo0.2290.0270.316
bin0.0140.0040.021
calcBinnedKmerEnr1.4540.0431.762
calcBinnedMotifEnrHomer0.0060.0190.053
calcBinnedMotifEnrR1.5770.2202.108
dumpJaspar0.0580.0110.102
findHomer0.0030.0100.015
findMotifHits-methods0.6260.0930.827
getColsByBin0.0070.0020.009
getKmerFreq0.0680.0100.088
getSetZeroBin0.0040.0010.005
homerToPFMatrixList0.1040.0180.150
motifKmerSimilarity0.0450.0080.070
motifSimilarity0.0200.0040.026
parseHomerOutput0.0160.0040.025
plotBinDensity0.0220.0040.030
plotBinDiagnostics1.450.131.85
plotBinHist0.0140.0020.020
plotBinScatter0.0110.0030.014
plotMotifHeatmaps10.278 0.17812.134
plotSelectionProb3.1120.0793.753
plotStabilityPaths1.3560.0161.601
prepareHomer0.1080.0080.134
randLassoStabSel2.9890.8983.158
sampleRandomRegions0.1140.0480.188
seqLogoGrob0.2970.0730.436