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This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 1974/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.26.0  (landing page)
Wanding Zhou
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_21
git_last_commit: bc933e0
git_last_commit_date: 2025-04-15 11:34:53 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for sesame on nebbiolo1

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: 1.26.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings sesame_1.26.0.tar.gz
StartedAt: 2025-10-16 03:34:09 -0400 (Thu, 16 Oct 2025)
EndedAt: 2025-10-16 03:51:01 -0400 (Thu, 16 Oct 2025)
EllapsedTime: 1012.3 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings sesame_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/sesame.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.26.0’
* 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 33.428  0.865  34.299
inferSex                      21.630  0.307  21.942
sesameQC_calcStats            18.394  1.284  19.679
imputeBetas                   17.455  0.563  18.022
sesameQC_plotHeatSNPs         16.075  0.252  16.330
inferSpecies                  15.384  0.818  16.206
diffRefSet                    13.731  0.403  14.137
ELBAR                         12.988  0.271  13.269
sesameQC_plotBar              11.646  0.515  12.162
compareReference              11.494  0.274  11.778
compareMouseStrainReference   11.147  0.253  11.403
getRefSet                     11.098  0.195  11.295
matchDesign                   10.618  0.191  10.815
sesameQC_plotBetaByDesign     10.148  0.357  10.508
visualizeGene                  8.668  0.318   8.989
DMR                            8.106  0.374   8.482
DML                            6.771  1.589   8.363
estimateLeukocyte              7.885  0.202   8.089
sdf_read_table                 7.501  0.189   7.690
inferStrain                    6.540  0.558   7.101
dyeBiasCorrMostBalanced        6.345  0.210   6.556
inferTissue                    5.970  0.310   6.282
getMask                        5.904  0.287   6.198
dyeBiasNL                      5.666  0.117   5.785
deidentify                     5.348  0.146   5.498
probeSuccessRate               5.201  0.219   5.420
createUCSCtrack                5.156  0.236   5.393
* 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-3.21-bioc/R/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘sesame’ ...
** this is package ‘sesame’ version ‘1.26.0’
** 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-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 
 18.090   1.045  19.127 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML6.7711.5898.363
DMLpredict1.3270.1121.439
DMR8.1060.3748.482
ELBAR12.988 0.27113.269
MValueToBetaValue000
SigDF0.2850.0440.329
addMask0.0680.0000.069
betasCollapseToPfx0.0120.0000.012
bisConversionControl4.3480.1664.516
calcEffectSize1.2290.1051.333
checkLevels2.9260.1233.051
cnSegmentation0.2620.0440.306
compareMouseStrainReference11.147 0.25311.403
compareMouseTissueReference000
compareReference11.494 0.27411.778
controls2.0630.1272.190
createUCSCtrack5.1560.2365.393
deidentify5.3480.1465.498
detectionPnegEcdf0.8830.0010.885
diffRefSet13.731 0.40314.137
dmContrasts2.0540.0962.153
dyeBiasCorr2.7280.1912.919
dyeBiasCorrMostBalanced6.3450.2106.556
dyeBiasL2.1060.0882.193
dyeBiasNL5.6660.1175.785
estimateLeukocyte7.8850.2028.089
formatVCF2.0570.1212.178
getAFTypeIbySumAlleles1.6310.1241.755
getAFs0.7540.0480.802
getBetas0.8460.0570.902
getMask5.9040.2876.198
getRefSet11.098 0.19511.295
imputeBetas17.455 0.56318.022
imputeBetasByGenomicNeighbors33.428 0.86534.299
imputeBetasMatrixByMean0.0010.0000.001
inferEthnicity0.0000.0000.001
inferInfiniumIChannel0.2790.5950.875
inferSex21.630 0.30721.942
inferSpecies15.384 0.81816.206
inferStrain6.5400.5587.101
inferTissue5.9700.3106.282
initFileSet1.2450.0891.334
listAvailableMasks1.2860.0731.359
mLiftOver0.0000.0010.001
mapFileSet0.0320.0010.033
mapToMammal402.7370.1862.926
matchDesign10.618 0.19110.815
meanIntensity2.6130.1462.759
medianTotalIntensity0.8070.0450.853
noMasked3.4360.1393.576
noob2.0050.0202.025
openSesame4.6840.1614.855
openSesameToFile1.3820.0041.388
pOOBAH1.2600.0091.269
palgen0.0370.0080.046
parseGEOsignalMU2.8750.0982.975
predictAge2.3870.1042.491
predictAgeHorvath353000
predictAgeSkinBlood0.0000.0010.000
predictMouseAgeInMonth000
prefixMask0.3720.0010.373
prefixMaskButC0.0940.0010.095
prefixMaskButCG0.0340.0000.034
prepSesame3.7860.1013.887
prepSesameList0.0020.0000.002
print.DMLSummary2.7720.2503.023
print.fileSet1.2030.0771.280
probeID_designType0.0010.0000.001
probeSuccessRate5.2010.2195.420
qualityMask1.9460.1422.087
reIdentify4.1650.0784.244
readFileSet0.0480.0030.051
readIDATpair0.0960.0010.097
recommendedMaskNames0.0000.0000.001
resetMask0.3690.0520.421
scrub2.0150.0162.030
scrubSoft3.1700.0093.179
sdfPlatform0.3020.0660.368
sdf_read_table7.5010.1897.690
sdf_write_table1.7020.0871.827
searchIDATprefixes0.0050.0090.015
sesame-package2.4090.2842.694
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download0.0000.0010.000
sesameAnno_readManifestTSV0.0000.0000.001
sesameQC_calcStats18.394 1.28419.679
sesameQC_getStats1.7320.0541.787
sesameQC_plotBar11.646 0.51512.162
sesameQC_plotBetaByDesign10.148 0.35710.508
sesameQC_plotHeatSNPs16.075 0.25216.330
sesameQC_plotIntensVsBetas1.9420.0872.029
sesameQC_plotRedGrnQQ1.6380.0651.703
sesameQC_rankStats3.5980.2083.833
sesameQCtoDF1.8340.0021.842
sesame_checkVersion0.0030.0010.004
sesamize000
setMask0.0920.0100.102
signalMU1.0690.1211.191
sliceFileSet0.0330.0010.034
summaryExtractTest2.8420.2343.076
totalIntensities2.3870.1612.547
updateSigDF3.1690.2123.383
visualizeGene8.6680.3188.989
visualizeProbes1.0680.0031.070
visualizeRegion0.3240.0050.329
visualizeSegments1.9540.0411.997