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This page was generated on 2025-10-18 12:04 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 1984/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 2025-10-18 04:41:52 -0400 (Sat, 18 Oct 2025)
EndedAt: 2025-10-18 04:57:38 -0400 (Sat, 18 Oct 2025)
EllapsedTime: 945.8 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 31.324  0.479  31.813
inferSex                      21.358  0.200  21.560
sesameQC_calcStats            17.120  0.179  17.299
imputeBetas                   16.072  0.415  16.513
sesameQC_plotHeatSNPs         15.407  0.197  15.606
inferSpecies                  14.572  0.788  15.361
diffRefSet                    13.548  0.198  13.746
ELBAR                         12.405  0.236  12.642
sesameQC_plotBar              11.633  0.206  11.840
matchDesign                   10.751  0.065  10.819
getRefSet                     10.604  0.077  10.681
compareMouseStrainReference   10.457  0.212  10.669
compareReference              10.055  0.272  10.328
visualizeGene                  8.710  0.147   8.857
sesameQC_plotBetaByDesign      8.313  0.112   8.426
DMR                            7.582  0.191   7.773
inferStrain                    6.807  0.441   7.251
sdf_read_table                 6.960  0.090   7.050
DML                            6.684  0.349   7.033
estimateLeukocyte              6.763  0.104   6.867
dyeBiasCorrMostBalanced        6.020  0.074   6.094
inferTissue                    5.856  0.136   5.993
getMask                        5.515  0.132   5.647
deIdentify                     5.178  0.092   5.271
dyeBiasNL                      5.126  0.126   5.254
createUCSCtrack                5.074  0.077   5.152
* 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 
 17.721   0.903  18.614 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML6.6840.3497.033
DMLpredict1.2120.0341.246
DMR7.5820.1917.773
ELBAR12.405 0.23612.642
MValueToBetaValue000
SigDF0.3060.0080.314
addMask0.0780.0000.078
betasCollapseToPfx0.0110.0000.011
bisConversionControl4.0640.0684.132
calcEffectSize1.2550.0291.284
checkLevels3.5890.0543.643
cnSegmentation0.2760.0170.294
compareMouseStrainReference10.457 0.21210.669
compareMouseTissueReference000
compareReference10.055 0.27210.328
controls1.9140.0421.956
createUCSCtrack5.0740.0775.152
deIdentify5.1780.0925.271
detectionPnegEcdf0.9320.0110.943
diffRefSet13.548 0.19813.746
dmContrasts1.7690.0301.800
dyeBiasCorr2.5380.0872.626
dyeBiasCorrMostBalanced6.0200.0746.094
dyeBiasL3.0080.0603.068
dyeBiasNL5.1260.1265.254
estimateLeukocyte6.7630.1046.867
formatVCF1.9680.0301.998
getAFTypeIbySumAlleles1.5080.0401.550
getAFs0.8610.0170.879
getBetas0.6730.0300.703
getMask5.5150.1325.647
getRefSet10.604 0.07710.681
imputeBetas16.072 0.41516.513
imputeBetasByGenomicNeighbors31.324 0.47931.813
imputeBetasMatrixByMean0.0010.0000.001
inferEthnicity0.0010.0000.001
inferInfiniumIChannel0.2380.0560.294
inferSex21.358 0.20021.560
inferSpecies14.572 0.78815.361
inferStrain6.8070.4417.251
inferTissue5.8560.1365.993
initFileSet1.0860.0341.120
listAvailableMasks1.1500.0241.174
mLiftOver000
mapFileSet0.0320.0010.033
mapToMammal402.3410.0652.407
matchDesign10.751 0.06510.819
meanIntensity2.3260.0602.387
medianTotalIntensity0.7730.0200.793
noMasked3.3940.0453.440
noob1.7070.0081.716
openSesame4.5920.1604.760
openSesameToFile1.2480.0081.259
pOOBAH1.1680.0021.170
palgen0.0300.0040.034
parseGEOsignalMU2.9140.0422.956
predictAge2.2540.0452.299
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.5460.0000.546
prefixMaskButC0.1690.0090.178
prefixMaskButCG0.0690.0090.078
prepSesame3.3420.0873.430
prepSesameList0.0010.0000.001
print.DMLSummary3.0130.1693.182
print.fileSet1.0950.0311.126
probeID_designType0.0010.0000.000
probeSuccessRate4.7770.1044.882
qualityMask2.0600.0572.117
reIdentify3.9120.0453.958
readFileSet0.0500.0010.051
readIDATpair0.1010.0010.102
recommendedMaskNames0.0000.0000.001
resetMask0.3420.0190.362
scrub2.0030.1302.133
scrubSoft3.0250.0273.052
sdfPlatform0.2710.0190.290
sdf_read_table6.960.097.05
sdf_write_table1.6400.0461.817
searchIDATprefixes0.0030.0010.006
sesame-package1.7780.0461.824
sesameAnno_attachManifest0.0000.0000.001
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats17.120 0.17917.299
sesameQC_getStats1.5340.0011.535
sesameQC_plotBar11.633 0.20611.840
sesameQC_plotBetaByDesign8.3130.1128.426
sesameQC_plotHeatSNPs15.407 0.19715.606
sesameQC_plotIntensVsBetas2.1530.0272.180
sesameQC_plotRedGrnQQ1.6290.0491.678
sesameQC_rankStats2.9910.0833.075
sesameQCtoDF1.5680.0201.588
sesame_checkVersion0.0030.0000.003
sesamize0.0010.0000.000
setMask0.0830.0010.083
signalMU0.6990.0230.722
sliceFileSet0.0330.0000.033
summaryExtractTest2.8200.1302.949
totalIntensities2.3190.0572.375
updateSigDF3.0250.1233.148
visualizeGene8.7100.1478.857
visualizeProbes0.9180.0020.919
visualizeRegion0.3090.0010.310
visualizeSegments1.7590.0121.771