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This page was generated on 2022-08-15 11:08:21 -0400 (Mon, 15 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4378
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4161
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4169
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 lconway


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 1820/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.15.6  (landing page)
Wanding Zhou
Snapshot Date: 2022-08-14 14:00:05 -0400 (Sun, 14 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
palomino4Windows Server 2022 Datacenter / x64  OK    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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sesame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sesame_1.15.6.tar.gz
StartedAt: 2022-08-14 22:26:02 -0400 (Sun, 14 Aug 2022)
EndedAt: 2022-08-14 22:40:44 -0400 (Sun, 14 Aug 2022)
EllapsedTime: 882.7 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sesame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sesame_1.15.6.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/sesame.Rcheck’
* using R version 4.2.1 Patched (2022-07-09 r82577)
* using platform: x86_64-apple-darwin17.0 (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
sesameQC_calcStats          29.414  1.654  34.512
KYCG_plotEnrichAll          26.646  1.018  28.881
sesameQC_plotHeatSNPs       25.514  1.546  27.247
inferSpecies                21.689  0.757  22.911
dyeBiasCorrMostBalanced     17.711  0.560  18.606
sesameQC_plotBar            14.937  0.792  15.951
getSexInfo                  14.838  0.700  15.945
KYCG_plotMeta               14.647  0.689  15.791
DMR                         14.777  0.450  15.471
diffRefSet                  13.710  0.625  14.546
probeSuccessRate            13.333  0.737  14.642
KYCG_plotMetaEnrichment     12.528  0.525  13.354
matchDesign                 12.504  0.522  13.194
sesameQC_plotBetaByDesign   11.040  1.133  12.201
inferStrain                 11.258  0.791  12.263
getRefSet                   11.448  0.523  12.167
compareMouseStrainReference 11.465  0.378  12.062
KYCG_annoProbes             11.321  0.451  11.988
dyeBiasCorr                 11.042  0.492  11.848
compareReference            10.108  0.549  10.839
KYCG_buildGeneDBs           10.164  0.404  10.757
testEnrichment               8.994  0.649   9.941
controls                     9.114  0.417   9.943
dbStats                      8.731  0.587   9.502
visualizeGene                8.831  0.481   9.646
detectionIB                  8.167  1.098   9.375
testEnrichmentSEA            8.436  0.723   9.658
inferSex                     7.909  0.521   8.610
prepSesame                   7.821  0.469   8.541
DML                          7.277  0.888   8.488
mapToMammal40                7.532  0.424   8.295
inferTissue                  6.707  1.249   8.204
formatVCF                    7.478  0.438   8.220
estimateLeukocyte            7.152  0.536   7.882
openSesame                   6.811  0.609   7.621
detectionPnegEcdf            7.025  0.357   7.555
dyeBiasNL                    6.390  0.469   6.980
noMasked                     5.996  0.143   6.393
KYCG_plotSetEnrichment       5.411  0.395   5.958
openSesameToFile             5.686  0.077   5.782
reIdentify                   5.212  0.396   5.703
bisConversionControl         5.364  0.210   5.733
createUCSCtrack              5.332  0.203   5.763
inferSexKaryotypes           5.218  0.276   5.586
sdf_read_table               5.139  0.244   5.504
deidentify                   5.113  0.237   5.526
scrubSoft                    4.576  0.545   5.143
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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 Patched (2022-07-09 r82577) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
 30.467   1.738  32.803 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML7.2770.8888.488
DMLpredict1.2510.0961.429
DMR14.777 0.45015.471
KYCG_annoProbes11.321 0.45111.988
KYCG_buildGeneDBs10.164 0.40410.757
KYCG_getDBs2.7490.1863.309
KYCG_listDBGroups0.0270.0010.028
KYCG_plotBar0.2390.0060.245
KYCG_plotDot0.2430.0050.248
KYCG_plotEnrichAll26.646 1.01828.881
KYCG_plotLollipop0.1170.0060.124
KYCG_plotManhattan1.2860.0971.384
KYCG_plotMeta14.647 0.68915.791
KYCG_plotMetaEnrichment12.528 0.52513.354
KYCG_plotPointRange3.1120.1733.376
KYCG_plotSetEnrichment5.4110.3955.958
KYCG_plotVolcano0.1540.0050.161
KYCG_plotWaterfall2.6730.1782.993
MValueToBetaValue0.0000.0000.001
SigDF0.2300.0340.331
addMask0.0750.0010.076
aggregateTestEnrichments2.4360.1362.583
bisConversionControl5.3640.2105.733
calcEffectSize0.9770.0881.136
checkLevels3.0270.2753.390
cnSegmentation0.2200.0400.325
compareMouseStrainReference11.465 0.37812.062
compareMouseTissueReference0.0000.0000.001
compareReference10.108 0.54910.839
controls9.1140.4179.943
createUCSCtrack5.3320.2035.763
dataFrame2sesameQC1.2130.1351.528
dbStats8.7310.5879.502
deidentify5.1130.2375.526
detectionIB8.1671.0989.375
detectionPnegEcdf7.0250.3577.555
diffRefSet13.710 0.62514.546
dmContrasts1.7900.1842.054
dyeBiasCorr11.042 0.49211.848
dyeBiasCorrMostBalanced17.711 0.56018.606
dyeBiasL2.4200.1162.606
dyeBiasNL6.3900.4696.980
estimateLeukocyte7.1520.5367.882
formatVCF7.4780.4388.220
getAFTypeIbySumAlleles1.3380.1381.627
getAFs1.1530.1241.359
getBetas0.9580.1421.179
getRefSet11.448 0.52312.167
getSexInfo14.838 0.70015.945
inferEthnicity3.5350.2343.850
inferInfiniumIChannel0.5910.4981.100
inferSex7.9090.5218.610
inferSexKaryotypes5.2180.2765.586
inferSpecies21.689 0.75722.911
inferStrain11.258 0.79112.263
inferTissue6.7071.2498.204
initFileSet1.0010.1901.267
listAvailableMasks1.6040.1261.810
mapFileSet0.0400.0030.043
mapToMammal407.5320.4248.295
matchDesign12.504 0.52213.194
meanIntensity2.8020.3673.320
medianTotalIntensity0.9840.0561.110
noMasked5.9960.1436.393
noob4.1070.4314.563
openSesame6.8110.6097.621
openSesameToFile5.6860.0775.782
pOOBAH3.4630.4293.930
palgen0.0520.0090.063
parseGEOsignalMU0.6100.0040.616
predictAge2.3130.1392.535
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth0.0000.0000.001
prefixMask0.4770.0010.479
prefixMaskButC0.1320.0000.132
prefixMaskButCG0.0660.0010.069
prepSesame7.8210.4698.541
prepSesameList0.0010.0010.003
print.DMLSummary2.8990.6963.788
print.fileSet1.0560.1591.292
probeID_designType000
probeSuccessRate13.333 0.73714.642
qualityMask3.6210.0573.765
reIdentify5.2120.3965.703
readFileSet0.0520.0110.065
readIDATpair0.1330.0030.137
resetMask0.3290.0470.444
scrub3.4540.3393.812
scrubSoft4.5760.5455.143
sdfPlatform1.2430.0681.388
sdf_read_table5.1390.2445.504
sdf_write_table2.2500.1272.515
searchIDATprefixes0.0030.0020.005
sesame-package3.5070.3594.053
sesameAnno_download000
sesameAnno_get000
sesameData_getAnno000
sesameQC_calcStats29.414 1.65434.512
sesameQC_getStats3.4390.1183.572
sesameQC_plotBar14.937 0.79215.951
sesameQC_plotBetaByDesign11.040 1.13312.201
sesameQC_plotHeatSNPs25.514 1.54627.247
sesameQC_plotIntensVsBetas2.1080.3402.539
sesameQC_plotRedGrnQQ1.0460.0821.197
sesameQC_rankStats3.1960.2523.795
setMask0.0890.0010.090
signalMU0.9550.2111.277
sliceFileSet0.0330.0030.035
summaryExtractTest2.6350.6003.380
testEnrichment8.9940.6499.941
testEnrichmentSEA8.4360.7239.658
totalIntensities4.1880.4884.829
updateSigDF2.6190.2633.027
visualizeGene8.8310.4819.646
visualizeProbes4.3580.2264.664
visualizeRegion0.3770.0030.380
visualizeSegments1.7830.3752.233