Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-19 12:11:32 -0400 (Fri, 19 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4387
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4177
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 sesame on nebbiolo2


To the developers/maintainers of the sesame package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sesame.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 1824/2144HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.15.6  (landing page)
Wanding Zhou
Snapshot Date: 2022-08-18 14:00:04 -0400 (Thu, 18 Aug 2022)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: master
git_last_commit: 5216376
git_last_commit_date: 2022-07-24 22:27:15 -0400 (Sun, 24 Jul 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: sesame
Version: 1.15.6
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings sesame_1.15.6.tar.gz
StartedAt: 2022-08-18 21:46:29 -0400 (Thu, 18 Aug 2022)
EndedAt: 2022-08-18 22:01:28 -0400 (Thu, 18 Aug 2022)
EllapsedTime: 899.0 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings sesame_1.15.6.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/sesame.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.15.6’
* 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 ‘sesame’ 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
KYCG_plotEnrichAll          27.406  2.929  32.073
sesameQC_calcStats          28.760  1.204  30.129
sesameQC_plotHeatSNPs       25.645  1.044  26.955
inferSpecies                20.605  1.793  23.246
dyeBiasCorrMostBalanced     17.662  1.112  19.444
DMR                         15.019  1.375  17.068
KYCG_plotMeta               15.109  0.952  16.657
getSexInfo                  13.843  0.708  15.493
matchDesign                 13.442  0.804  14.408
sesameQC_plotBar            13.518  0.721  14.614
KYCG_annoProbes             12.896  1.304  14.806
diffRefSet                  12.931  1.027  14.287
probeSuccessRate            12.804  0.888  14.777
sesameQC_plotBetaByDesign   13.278  0.404  13.682
compareMouseStrainReference 11.856  0.972  13.155
KYCG_plotMetaEnrichment     11.360  0.709  12.662
dyeBiasCorr                 11.222  0.783  12.844
compareReference            10.637  1.144  12.112
getRefSet                   10.916  0.844  12.191
KYCG_buildGeneDBs           10.552  0.889  11.860
inferStrain                 10.051  0.761  11.244
testEnrichmentSEA            9.963  0.752  11.521
testEnrichment               9.738  0.801  11.497
visualizeGene                9.482  0.711  10.780
dbStats                      8.707  0.936   9.974
controls                     8.903  0.696  10.539
dyeBiasNL                    7.694  1.064   9.016
DML                          7.545  0.704   8.670
inferTissue                  7.616  0.616   8.583
estimateLeukocyte            7.116  0.972   8.514
detectionIB                  7.335  0.669   8.320
prepSesame                   7.114  0.688   8.219
formatVCF                    7.181  0.516   8.462
mapToMammal40                6.953  0.424   7.962
openSesame                   6.676  0.540   7.654
detectionPnegEcdf            6.613  0.412   7.349
inferSex                     6.266  0.368   7.061
sesameQC_rankStats           5.873  0.620   6.907
bisConversionControl         5.839  0.579   6.746
noMasked                     5.778  0.467   6.762
KYCG_plotSetEnrichment       5.297  0.584   6.312
inferSexKaryotypes           5.450  0.384   6.000
reIdentify                   5.357  0.416   6.024
deidentify                   5.153  0.408   6.005
openSesameToFile             5.132  0.384   5.516
createUCSCtrack              5.162  0.352   5.841
sdf_read_table               5.237  0.212   5.711
* 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

sesame.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘sesame’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (sesame)

Tests output

sesame.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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(sesame)
Loading required package: sesameData
Loading required package: ExperimentHub
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading sesameData.

----------------------------------------------------------
| SEnsible Step-wise Analysis of DNA MEthylation (SeSAMe)
| --------------------------------------------------------
| Please cache auxiliary data by "sesameDataCache()".
| This needs to be done only once per SeSAMe installation.
----------------------------------------------------------

> 
> test_check("sesame")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 30.039   2.243  33.028 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML7.5450.7048.670
DMLpredict1.2370.1001.592
DMR15.019 1.37517.068
KYCG_annoProbes12.896 1.30414.806
KYCG_buildGeneDBs10.552 0.88911.860
KYCG_getDBs3.2070.3794.045
KYCG_listDBGroups0.0300.0040.034
KYCG_plotBar0.2860.0360.322
KYCG_plotDot0.2150.0160.231
KYCG_plotEnrichAll27.406 2.92932.073
KYCG_plotLollipop0.1090.0160.125
KYCG_plotManhattan1.4050.1361.541
KYCG_plotMeta15.109 0.95216.657
KYCG_plotMetaEnrichment11.360 0.70912.662
KYCG_plotPointRange3.4810.3033.947
KYCG_plotSetEnrichment5.2970.5846.312
KYCG_plotVolcano0.1420.0200.162
KYCG_plotWaterfall2.5990.2843.049
MValueToBetaValue000
SigDF0.5650.0920.824
addMask0.0850.0040.089
aggregateTestEnrichments1.9200.1722.092
bisConversionControl5.8390.5796.746
calcEffectSize1.2530.1321.551
checkLevels3.5020.4684.238
cnSegmentation0.3490.0120.526
compareMouseStrainReference11.856 0.97213.155
compareMouseTissueReference000
compareReference10.637 1.14412.112
controls 8.903 0.69610.539
createUCSCtrack5.1620.3525.841
dataFrame2sesameQC1.1410.1361.543
dbStats8.7070.9369.974
deidentify5.1530.4086.005
detectionIB7.3350.6698.320
detectionPnegEcdf6.6130.4127.349
diffRefSet12.931 1.02714.287
dmContrasts2.0010.2082.464
dyeBiasCorr11.222 0.78312.844
dyeBiasCorrMostBalanced17.662 1.11219.444
dyeBiasL2.1200.3042.693
dyeBiasNL7.6941.0649.016
estimateLeukocyte7.1160.9728.514
formatVCF7.1810.5168.462
getAFTypeIbySumAlleles1.3990.1692.091
getAFs1.0440.1361.435
getBetas0.9190.1291.301
getRefSet10.916 0.84412.191
getSexInfo13.843 0.70815.493
inferEthnicity3.7870.2654.224
inferInfiniumIChannel0.4320.1640.596
inferSex6.2660.3687.061
inferSexKaryotypes5.4500.3846.000
inferSpecies20.605 1.79323.246
inferStrain10.051 0.76111.244
inferTissue7.6160.6168.583
initFileSet1.0880.0841.353
listAvailableMasks1.6510.1202.040
mapFileSet0.0340.0000.034
mapToMammal406.9530.4247.962
matchDesign13.442 0.80414.408
meanIntensity2.9570.2803.654
medianTotalIntensity0.8990.1161.178
noMasked5.7780.4676.762
noob3.3320.2523.585
openSesame6.6760.5407.654
openSesameToFile5.1320.3845.516
pOOBAH2.7530.0922.845
palgen0.0280.0200.048
parseGEOsignalMU0.5970.0240.621
predictAge2.3140.1922.777
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.4510.0200.471
prefixMaskButC0.1030.0160.119
prefixMaskButCG0.0400.0000.039
prepSesame7.1140.6888.219
prepSesameList0.0020.0000.002
print.DMLSummary3.2390.5404.197
print.fileSet1.1250.0561.346
probeID_designType0.0010.0000.000
probeSuccessRate12.804 0.88814.777
qualityMask3.2760.2323.671
reIdentify5.3570.4166.024
readFileSet0.0490.0040.054
readIDATpair0.1190.0120.130
resetMask0.3760.0520.592
scrub3.5170.3923.908
scrubSoft4.5550.2804.835
sdfPlatform1.1680.0441.377
sdf_read_table5.2370.2125.711
sdf_write_table2.6210.1603.042
searchIDATprefixes0.0010.0130.015
sesame-package3.3820.3153.960
sesameAnno_download000
sesameAnno_get000
sesameData_getAnno000
sesameQC_calcStats28.760 1.20430.129
sesameQC_getStats2.7540.0512.806
sesameQC_plotBar13.518 0.72114.614
sesameQC_plotBetaByDesign13.278 0.40413.682
sesameQC_plotHeatSNPs25.645 1.04426.955
sesameQC_plotIntensVsBetas2.8370.2433.343
sesameQC_plotRedGrnQQ2.1480.1482.561
sesameQC_rankStats5.8730.6206.907
setMask0.1160.0000.116
signalMU0.9240.1041.293
sliceFileSet0.0300.0060.037
summaryExtractTest3.2380.3173.974
testEnrichment 9.738 0.80111.497
testEnrichmentSEA 9.963 0.75211.521
totalIntensities2.7210.2003.337
updateSigDF4.1610.3844.974
visualizeGene 9.482 0.71110.780
visualizeProbes3.9190.2924.463
visualizeRegion0.3340.0120.347
visualizeSegments2.4140.4043.070