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This page was generated on 2025-10-28 12:03 -0400 (Tue, 28 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
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 1992/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-10-27 13:45 -0400 (Mon, 27 Oct 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
lconwaymacOS 12.7.6 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


CHECK results for sesame on nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings sesame_1.27.1.tar.gz
StartedAt: 2025-10-28 04:05:32 -0400 (Tue, 28 Oct 2025)
EndedAt: 2025-10-28 04:22:04 -0400 (Tue, 28 Oct 2025)
EllapsedTime: 992.0 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings sesame_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/sesame.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 33.690  0.682  34.373
inferSex                      20.358  0.212  20.572
sesameQC_plotHeatSNPs         17.671  0.208  17.880
imputeBetas                   17.377  0.425  17.808
sesameQC_calcStats            17.422  0.148  17.572
inferSpecies                  15.716  0.663  16.380
diffRefSet                    14.795  0.339  15.135
ELBAR                         13.903  0.180  14.086
getRefSet                     12.260  0.173  12.432
sesameQC_plotBar              11.418  0.264  12.131
compareMouseStrainReference   11.307  0.092  11.399
compareReference              10.989  0.254  11.245
matchDesign                   10.719  0.151  10.876
sesameQC_plotBetaByDesign      9.187  0.141   9.329
inferStrain                    8.464  0.601   9.067
visualizeGene                  8.664  0.233   8.898
DMR                            8.318  0.211   8.530
sdf_read_table                 7.331  0.098   7.429
DML                            6.860  0.340   7.203
estimateLeukocyte              6.617  0.123   6.740
deIdentify                     6.621  0.101   6.724
dyeBiasCorrMostBalanced        6.468  0.102   6.569
inferTissue                    6.280  0.187   6.468
getMask                        6.055  0.128   6.185
createUCSCtrack                5.429  0.177   5.606
openSesame                     5.291  0.166   5.464
dyeBiasNL                      5.313  0.075   5.390
probeSuccessRate               5.118  0.100   5.218
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

sesame.Rcheck/00install.out

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 18.679   1.097  19.766 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML6.8600.3407.203
DMLpredict1.2990.0431.341
DMR8.3180.2118.530
ELBAR13.903 0.18014.086
MValueToBetaValue000
SigDF0.3000.0070.307
addMask0.0830.0000.082
betasCollapseToPfx0.0110.0000.011
bisConversionControl4.3220.0714.393
calcEffectSize1.2260.0271.254
checkLevels3.0540.0433.097
cnSegmentation0.2730.0120.285
compareMouseStrainReference11.307 0.09211.399
compareMouseTissueReference000
compareReference10.989 0.25411.245
controls2.0740.0682.141
createUCSCtrack5.4290.1775.606
deIdentify6.6210.1016.724
detectionPnegEcdf0.8940.0190.913
diffRefSet14.795 0.33915.135
dmContrasts2.0640.0352.098
dyeBiasCorr2.8070.1082.915
dyeBiasCorrMostBalanced6.4680.1026.569
dyeBiasL2.2420.0642.306
dyeBiasNL5.3130.0755.390
estimateLeukocyte6.6170.1236.740
formatVCF2.1410.0412.183
getAFTypeIbySumAlleles1.7280.0501.779
getAFs1.0120.0121.024
getBetas0.7720.0210.792
getMask6.0550.1286.185
getRefSet12.260 0.17312.432
imputeBetas17.377 0.42517.808
imputeBetasByGenomicNeighbors33.690 0.68234.373
imputeBetasMatrixByMean0.0020.0000.001
inferEthnicity0.0010.0000.001
inferInfiniumIChannel0.2500.0590.308
inferSex20.358 0.21220.572
inferSpecies15.716 0.66316.380
inferStrain8.4640.6019.067
inferTissue6.2800.1876.468
initFileSet1.1830.0281.211
listAvailableMasks1.2260.0301.256
mLiftOver000
mapFileSet0.0310.0020.033
mapToMammal402.7980.0672.865
matchDesign10.719 0.15110.876
meanIntensity2.7760.0862.862
medianTotalIntensity0.9260.0440.971
noMasked3.6370.1003.737
noob1.9070.0151.922
openSesame5.2910.1665.464
openSesameToFile1.3450.0271.374
pOOBAH1.2650.0181.283
palgen0.0450.0030.048
parseGEOsignalMU3.0970.0843.181
predictAge2.5080.0492.557
predictAgeHorvath3530.0000.0000.001
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.420.000.42
prefixMaskButC0.1290.0020.130
prefixMaskButCG0.0520.0000.051
prepSesame3.9440.0704.015
prepSesameList0.0010.0000.001
print.DMLSummary3.1290.1173.245
print.fileSet1.2200.0261.245
probeID_designType0.0010.0000.000
probeSuccessRate5.1180.1005.218
qualityMask2.0390.0632.102
reIdentify4.0720.0434.115
readFileSet0.0510.0020.053
readIDATpair0.1020.0000.103
recommendedMaskNames000
resetMask0.3530.0180.370
scrub2.0600.0582.118
scrubSoft3.3940.1123.505
sdfPlatform0.3010.0160.317
sdf_read_table7.3310.0987.429
sdf_write_table1.6700.0401.847
searchIDATprefixes0.0020.0010.005
sesame-package2.2750.0722.349
sesameAnno_attachManifest0.0000.0010.000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats17.422 0.14817.572
sesameQC_getStats1.6380.0051.643
sesameQC_plotBar11.418 0.26412.131
sesameQC_plotBetaByDesign9.1870.1419.329
sesameQC_plotHeatSNPs17.671 0.20817.880
sesameQC_plotIntensVsBetas1.8070.0921.899
sesameQC_plotRedGrnQQ1.6210.0331.654
sesameQC_rankStats3.0310.0883.120
sesameQCtoDF1.5730.0081.581
sesame_checkVersion0.0040.0000.004
sesamize0.0010.0000.000
setMask0.0880.0000.088
signalMU0.7120.0320.744
sliceFileSet0.0330.0000.034
summaryExtractTest2.7870.1482.935
totalIntensities2.3640.0512.415
updateSigDF3.1020.1103.212
visualizeGene8.6640.2338.898
visualizeProbes1.1210.0041.126
visualizeRegion0.3180.0030.321
visualizeSegments1.8340.0601.893