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This page was generated on 2025-08-14 12:09 -0400 (Thu, 14 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 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 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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: 2025-08-13 13:45 -0400 (Wed, 13 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 24.04.3 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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for sesame on lconway

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: 2025-08-13 23:42:43 -0400 (Wed, 13 Aug 2025)
EndedAt: 2025-08-13 23:55:30 -0400 (Wed, 13 Aug 2025)
EllapsedTime: 766.8 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_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/sesame.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 37.610  1.449  39.294
inferSex                      24.076  1.137  25.302
sesameQC_calcStats            22.835  1.334  24.312
sesameQC_plotHeatSNPs         20.055  1.506  21.709
imputeBetas                   18.718  1.456  20.305
ELBAR                         16.641  2.845  19.638
diffRefSet                    16.500  0.625  17.227
sesameQC_plotBar              14.681  0.687  15.474
inferSpecies                  13.704  0.681  14.479
compareMouseStrainReference   13.081  0.416  13.621
getRefSet                     12.964  0.469  13.506
compareReference              11.992  0.536  12.627
sesameQC_plotBetaByDesign     10.799  1.449  12.353
matchDesign                   10.529  0.755  11.354
visualizeGene                  9.608  0.696  10.390
DML                            8.626  1.243   9.950
DMR                            9.097  0.292   9.456
sdf_read_table                 8.937  0.387   9.395
estimateLeukocyte              8.288  0.560   8.897
inferTissue                    7.035  1.313   8.397
inferStrain                    7.746  0.588   8.382
getMask                        6.765  0.645   7.459
dyeBiasCorrMostBalanced        7.025  0.295   7.367
dyeBiasNL                      6.317  0.475   6.829
deIdentify                     6.158  0.318   6.539
reIdentify                     6.040  0.229   6.308
createUCSCtrack                5.927  0.340   6.305
probeSuccessRate               5.703  0.483   6.225
openSesame                     5.387  0.538   5.980
sesameQC_rankStats             5.083  0.638   5.783
bisConversionControl           4.846  0.265   5.170
* 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-x86_64/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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 
 22.418   1.864  24.403 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0010.0000.001
DML8.6261.2439.950
DMLpredict1.3110.1061.423
DMR9.0970.2929.456
ELBAR16.641 2.84519.638
MValueToBetaValue0.0000.0000.001
SigDF0.3130.0970.419
addMask0.0730.0000.074
betasCollapseToPfx0.0110.0000.011
bisConversionControl4.8460.2655.170
calcEffectSize1.2530.1581.452
checkLevels4.0320.2374.313
cnSegmentation0.3010.0550.359
compareMouseStrainReference13.081 0.41613.621
compareMouseTissueReference000
compareReference11.992 0.53612.627
controls2.1040.2552.374
createUCSCtrack5.9270.3406.305
deIdentify6.1580.3186.539
detectionPnegEcdf1.3060.0151.327
diffRefSet16.500 0.62517.227
dmContrasts2.0910.2252.334
dyeBiasCorr2.9220.2213.167
dyeBiasCorrMostBalanced7.0250.2957.367
dyeBiasL2.3510.1112.473
dyeBiasNL6.3170.4756.829
estimateLeukocyte8.2880.5608.897
formatVCF2.2710.2662.549
getAFTypeIbySumAlleles1.9000.2122.127
getAFs0.9440.0601.008
getBetas0.9050.1311.041
getMask6.7650.6457.459
getRefSet12.964 0.46913.506
imputeBetas18.718 1.45620.305
imputeBetasByGenomicNeighbors37.610 1.44939.294
imputeBetasMatrixByMean0.0010.0000.001
inferEthnicity0.0010.0000.001
inferInfiniumIChannel0.3990.4910.895
inferSex24.076 1.13725.302
inferSpecies13.704 0.68114.479
inferStrain7.7460.5888.382
inferTissue7.0351.3138.397
initFileSet1.2500.2501.519
listAvailableMasks1.3240.1481.482
mLiftOver0.0000.0020.002
mapFileSet0.0360.0060.042
mapToMammal403.1650.3963.588
matchDesign10.529 0.75511.354
meanIntensity2.6030.1972.818
medianTotalIntensity0.9020.0640.973
noMasked3.9910.2254.242
noob2.3770.5192.915
openSesame5.3870.5385.980
openSesameToFile1.7100.2211.947
pOOBAH1.3860.0101.407
palgen0.0410.0070.049
parseGEOsignalMU3.1400.1503.315
predictAge2.6260.1402.793
predictAgeHorvath353000
predictAgeSkinBlood0.0000.0010.000
predictMouseAgeInMonth000
prefixMask0.6010.0040.608
prefixMaskButC0.1650.0020.170
prefixMaskButCG0.0630.0000.064
prepSesame3.8430.3634.232
prepSesameList0.0010.0010.001
print.DMLSummary3.1750.9454.157
print.fileSet1.2910.2301.530
probeID_designType0.0000.0010.000
probeSuccessRate5.7030.4836.225
qualityMask2.2710.3422.633
reIdentify6.0400.2296.308
readFileSet0.0610.0040.065
readIDATpair0.1570.0020.161
recommendedMaskNames0.0000.0000.001
resetMask0.4060.0710.481
scrub2.4370.3142.763
scrubSoft3.3230.6714.012
sdfPlatform0.2980.0870.386
sdf_read_table8.9370.3879.395
sdf_write_table2.6800.1542.850
searchIDATprefixes0.0030.0020.005
sesame-package2.5230.3342.867
sesameAnno_attachManifest0.0000.0000.001
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download0.0000.0000.001
sesameAnno_readManifestTSV000
sesameQC_calcStats22.835 1.33424.312
sesameQC_getStats2.4360.0822.536
sesameQC_plotBar14.681 0.68715.474
sesameQC_plotBetaByDesign10.799 1.44912.353
sesameQC_plotHeatSNPs20.055 1.50621.709
sesameQC_plotIntensVsBetas2.1990.4112.637
sesameQC_plotRedGrnQQ1.1330.1331.277
sesameQC_rankStats5.0830.6385.783
sesameQCtoDF2.0970.0122.120
sesame_checkVersion0.0030.0010.004
sesamize000
setMask0.1000.0010.100
signalMU1.1130.3131.444
sliceFileSet0.0350.0100.045
summaryExtractTest2.6910.6033.333
totalIntensities2.5230.3702.920
updateSigDF3.1500.3563.531
visualizeGene 9.608 0.69610.390
visualizeProbes1.3350.0301.373
visualizeRegion0.3870.0040.394
visualizeSegments1.7090.3542.079