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This page was generated on 2022-04-13 12:06:55 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 tokay2


To the developers/maintainers of the monaLisa package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/monaLisa.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1194/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
monaLisa 1.0.0  (landing page)
Michael Stadler
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/monaLisa
git_branch: RELEASE_3_14
git_last_commit: bec40ca
git_last_commit_date: 2021-10-26 13:12:48 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: monaLisa
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:monaLisa.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings monaLisa_1.0.0.tar.gz
StartedAt: 2022-04-12 23:09:29 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 23:17:15 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 466.1 seconds
RetCode: 0
Status:   OK  
CheckDir: monaLisa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:monaLisa.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings monaLisa_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/monaLisa.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'monaLisa/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'monaLisa' version '1.0.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
plotMotifHeatmaps 5.03   0.09    5.15
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
plotMotifHeatmaps 5.64   0.06    5.71
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

monaLisa.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/monaLisa_1.0.0.tar.gz && rm -rf monaLisa.buildbin-libdir && mkdir monaLisa.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=monaLisa.buildbin-libdir monaLisa_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL monaLisa_1.0.0.zip && rm monaLisa_1.0.0.tar.gz monaLisa_1.0.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 13 2707k   13  367k    0     0   752k      0  0:00:03 --:--:--  0:00:03  753k
 68 2707k   68 1867k    0     0  1284k      0  0:00:02  0:00:01  0:00:01 1284k
100 2707k  100 2707k    0     0  1482k      0  0:00:01  0:00:01 --:--:-- 1482k

install for i386

* installing *source* package 'monaLisa' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'monaLisa'
    finding HTML links ... done
    annoSeqlogo                             html  
    bin                                     html  
    calcBinnedKmerEnr                       html  
    calcBinnedMotifEnrHomer                 html  
    calcBinnedMotifEnrR                     html  
    dot-calcKmerEnrichment                  html  
    dot-calcMotifEnrichment                 html  
    dot-calculateGCweight                   html  
    dot-checkDfValidity                     html  
    dot-checkIfSeqsAreEqualLength           html  
    dot-cons2matrix                         html  
    dot-defineBackground                    html  
    dot-filterSeqs                          html  
    dot-glmnetRandomizedLasso               html  
    dot-iterativeNormForKmers               html  
    dot-normForKmers                        html  
    dumpJaspar                              html  
    findHomer                               html  
    findMotifHits-methods                   html  
    getColsByBin                            html  
    getKmerFreq                             html  
    finding level-2 HTML links ... done

    getSetZeroBin                           html  
    homerToPFMatrixList                     html  
    monaLisa-package                        html  
    motifKmerSimilarity                     html  
    motifSimilarity                         html  
    parseHomerOutput                        html  
    plotBinDensity                          html  
    plotBinDiagnostics                      html  
    plotBinHist                             html  
    plotBinScatter                          html  
    plotMotifHeatmaps                       html  
    plotSelectionProb                       html  
    plotStabilityPaths                      html  
    prepareHomer                            html  
    randLassoStabSel                        html  
    sampleRandomRegions                     html  
    seqLogoGrob                             html  
*** 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

install for x64

* installing *source* package 'monaLisa' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'monaLisa' as monaLisa_1.0.0.zip
* DONE (monaLisa)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'monaLisa' successfully unpacked and MD5 sums checked

Tests output

monaLisa.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 2 | PASS 533 ]

== Skipped tests ===============================================================
* On Windows (1)
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 533 ]
> 
> proc.time()
   user  system elapsed 
  42.25    2.10   44.37 

monaLisa.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 2 | PASS 533 ]

== Skipped tests ===============================================================
* On Windows (1)
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 533 ]
> 
> proc.time()
   user  system elapsed 
  51.28    1.06   52.32 

Example timings

monaLisa.Rcheck/examples_i386/monaLisa-Ex.timings

nameusersystemelapsed
annoSeqlogo0.140.050.18
bin000
calcBinnedKmerEnr0.670.210.90
calcBinnedMotifEnrHomer000
calcBinnedMotifEnrR0.690.250.93
dumpJaspar0.030.000.08
findHomer000
findMotifHits-methods0.420.000.42
getColsByBin0.020.000.02
getKmerFreq0.030.000.03
getSetZeroBin000
homerToPFMatrixList0.060.000.06
motifKmerSimilarity0.020.000.02
motifSimilarity0.010.000.01
parseHomerOutput0.020.000.02
plotBinDensity0.010.000.01
plotBinDiagnostics0.710.070.77
plotBinHist0.010.000.02
plotBinScatter000
plotMotifHeatmaps5.030.095.15
plotSelectionProb0.850.060.91
plotStabilityPaths0.620.080.70
prepareHomer0.050.000.05
randLassoStabSel0.610.000.61
sampleRandomRegions0.060.000.06
seqLogoGrob0.220.020.25

monaLisa.Rcheck/examples_x64/monaLisa-Ex.timings

nameusersystemelapsed
annoSeqlogo0.130.030.15
bin000
calcBinnedKmerEnr0.740.080.81
calcBinnedMotifEnrHomer000
calcBinnedMotifEnrR0.820.070.91
dumpJaspar0.020.000.02
findHomer000
findMotifHits-methods0.30.00.3
getColsByBin000
getKmerFreq0.030.000.03
getSetZeroBin000
homerToPFMatrixList0.060.000.06
motifKmerSimilarity0.020.000.01
motifSimilarity0.010.000.02
parseHomerOutput000
plotBinDensity000
plotBinDiagnostics0.70.00.7
plotBinHist0.020.000.01
plotBinScatter000
plotMotifHeatmaps5.640.065.71
plotSelectionProb0.970.020.98
plotStabilityPaths0.680.000.69
prepareHomer0.100.000.12
randLassoStabSel0.840.000.85
sampleRandomRegions0.080.000.08
seqLogoGrob0.200.010.22