Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 1956/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: devel
git_last_commit: e90f911
git_last_commit_date: 2025-06-21 02:29:58 -0400 (Sat, 21 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for sesame on kjohnson3

To the developers/maintainers of the sesame package:
- 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 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: sesame
Version: 1.27.1
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_1.27.1.tar.gz
StartedAt: 2025-08-08 21:35:57 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 21:40:35 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 277.5 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/sesame.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.27.1’
* 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 code 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 whether startup messages can be suppressed ... 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
imputeBetasByGenomicNeighbors 13.989  0.539  14.570
inferSex                       9.464  0.450   9.943
sesameQC_calcStats             7.944  0.707   8.658
sesameQC_plotHeatSNPs          7.864  0.769   8.643
imputeBetas                    7.005  0.594   7.623
inferSpecies                   6.746  0.293   7.047
ELBAR                          5.607  1.102   6.747
sesameQC_plotBar               5.910  0.180   6.111
diffRefSet                     5.767  0.183   5.953
getRefSet                      5.111  0.136   5.263
* 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

sesame.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘sesame’ ...
** this is package ‘sesame’ version ‘1.27.1’
** 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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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(sesame)
Loading required package: sesameData
Loading required package: ExperimentHub
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 5 ]
> 
> proc.time()
   user  system elapsed 
  8.342   0.444   8.788 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML2.6310.3463.002
DMLpredict0.3980.0350.441
DMR2.9870.0923.083
ELBAR5.6071.1026.747
MValueToBetaValue000
SigDF0.0890.0150.105
addMask0.0200.0010.021
betasCollapseToPfx0.0040.0000.004
bisConversionControl2.2310.0662.301
calcEffectSize0.3670.0310.397
checkLevels1.5500.0741.629
cnSegmentation0.0790.0130.093
compareMouseStrainReference3.6950.1473.870
compareMouseTissueReference000
compareReference4.2970.1294.443
controls0.7340.0600.797
createUCSCtrack2.2010.1062.339
deIdentify1.9690.0902.111
detectionPnegEcdf0.4000.0090.413
diffRefSet5.7670.1835.953
dmContrasts0.6900.0580.751
dyeBiasCorr0.9810.1001.083
dyeBiasCorrMostBalanced3.2790.0893.397
dyeBiasL0.7920.0530.846
dyeBiasNL2.0130.1892.209
estimateLeukocyte2.6400.1742.823
formatVCF0.7790.0920.880
getAFTypeIbySumAlleles0.5740.0590.634
getAFs0.3250.0520.377
getBetas0.2930.0400.334
getMask2.5590.2072.777
getRefSet5.1110.1365.263
imputeBetas7.0050.5947.623
imputeBetasByGenomicNeighbors13.989 0.53914.570
imputeBetasMatrixByMean0.0000.0000.001
inferEthnicity000
inferInfiniumIChannel0.1320.1510.292
inferSex9.4640.4509.943
inferSpecies6.7460.2937.047
inferStrain3.6140.2533.891
inferTissue2.4050.3312.737
initFileSet0.3690.0950.464
listAvailableMasks0.4220.0860.509
mLiftOver0.0000.0010.000
mapFileSet0.0160.0020.018
mapToMammal400.8990.1761.079
matchDesign4.3820.3254.737
meanIntensity0.9010.1081.010
medianTotalIntensity0.2680.0510.319
noMasked1.3120.0941.413
noob0.9030.1511.081
openSesame1.7290.2261.965
openSesameToFile0.5870.0780.676
pOOBAH0.5480.0290.582
palgen0.0150.0020.017
parseGEOsignalMU1.2700.1371.411
predictAge1.0390.0421.093
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.2120.0030.215
prefixMaskButC0.0520.0010.053
prefixMaskButCG0.0210.0010.022
prepSesame1.3710.1511.541
prepSesameList0.0000.0000.001
print.DMLSummary1.1070.1551.283
print.fileSet0.3810.0470.474
probeID_designType000
probeSuccessRate2.0000.2002.208
qualityMask0.6650.1310.798
reIdentify1.7110.1711.888
readFileSet0.0260.0010.029
readIDATpair0.0390.0060.044
recommendedMaskNames000
resetMask0.1030.0160.127
scrub0.9330.1211.054
scrubSoft1.3530.2351.590
sdfPlatform0.0850.0150.099
sdf_read_table3.7430.2484.027
sdf_write_table0.9220.0430.970
searchIDATprefixes0.0010.0000.003
sesame-package0.9420.0711.015
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV0.0010.0000.000
sesameQC_calcStats7.9440.7078.658
sesameQC_getStats0.7990.0420.840
sesameQC_plotBar5.9100.1806.111
sesameQC_plotBetaByDesign3.6280.6734.327
sesameQC_plotHeatSNPs7.8640.7698.643
sesameQC_plotIntensVsBetas0.6280.1240.756
sesameQC_plotRedGrnQQ0.4460.0610.512
sesameQC_rankStats1.7130.2611.989
sesameQCtoDF0.7830.0290.815
sesame_checkVersion0.0010.0010.001
sesamize000
setMask0.0210.0010.022
signalMU0.2520.0400.292
sliceFileSet0.0150.0010.018
summaryExtractTest1.0810.1171.207
totalIntensities0.8510.1200.971
updateSigDF1.0630.1651.232
visualizeGene3.5970.2063.814
visualizeProbes0.3930.0080.400
visualizeRegion0.1200.0050.125
visualizeSegments0.8390.1120.960