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This page was generated on 2023-04-12 10:55:27 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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

CHECK results for monaLisa on nebbiolo1


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1264/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
monaLisa 1.5.0  (landing page)
Michael Stadler
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/monaLisa
git_branch: devel
git_last_commit: e24b24c
git_last_commit_date: 2022-11-01 11:25:44 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

Summary

Package: monaLisa
Version: 1.5.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:monaLisa.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings monaLisa_1.5.0.tar.gz
StartedAt: 2023-04-11 21:42:21 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 21:52:15 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 594.1 seconds
RetCode: 0
Status:   OK  
CheckDir: monaLisa.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:monaLisa.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings monaLisa_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/monaLisa.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘monaLisa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘monaLisa’ version ‘1.5.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 ...
  ‘monaLisa.Rmd’ using ‘UTF-8’... OK
  ‘selecting_motifs_with_randLassoStabSel.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

monaLisa.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL monaLisa
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(monaLisa)

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

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 537 ]
> 
> proc.time()
   user  system elapsed 
 58.785   7.316  64.677 

Example timings

monaLisa.Rcheck/monaLisa-Ex.timings

nameusersystemelapsed
annoSeqlogo0.2070.0110.226
bin0.0070.0020.009
calcBinnedKmerEnr0.8630.0760.939
calcBinnedMotifEnrHomer0.0050.0010.005
calcBinnedMotifEnrR0.7180.1080.827
dumpJaspar0.0340.0000.035
findHomer0.0000.0030.004
findMotifHits-methods1.5110.0681.578
getColsByBin0.0040.0000.004
getKmerFreq0.0320.0000.031
getSetZeroBin0.0030.0000.002
homerToPFMatrixList0.0600.0040.064
motifKmerSimilarity0.0220.0000.022
motifSimilarity0.0080.0000.009
parseHomerOutput0.010.000.01
plotBinDensity0.0150.0000.015
plotBinDiagnostics0.5780.0000.578
plotBinHist0.0090.0000.009
plotBinScatter0.0080.0000.008
plotMotifHeatmaps4.1900.0644.254
plotSelectionProb0.9560.0601.016
plotStabilityPaths0.7530.0480.800
prepareHomer0.0530.0120.065
randLassoStabSel0.7450.0871.374
sampleRandomRegions0.8060.4510.051
seqLogoGrob0.1770.0320.211