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This page was generated on 2025-08-23 12:04 -0400 (Sat, 23 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4599
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 1958/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-08-22 13:45 -0400 (Fri, 22 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
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 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: 2025-08-23 02:45:25 -0400 (Sat, 23 Aug 2025)
EndedAt: 2025-08-23 03:01:41 -0400 (Sat, 23 Aug 2025)
EllapsedTime: 976.0 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 (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 ‘1.27.1’
* 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 33.280  0.576  33.859
inferSex                      19.277  0.182  19.461
sesameQC_calcStats            17.730  0.191  17.922
imputeBetas                   16.708  0.440  17.152
sesameQC_plotHeatSNPs         16.309  0.231  16.541
diffRefSet                    13.475  0.316  13.791
ELBAR                         13.302  0.249  13.552
inferSpecies                  12.830  0.617  13.447
compareMouseStrainReference   11.716  0.126  11.845
sesameQC_plotBar              11.522  0.216  11.738
getRefSet                     10.934  0.074  11.008
compareReference              10.470  0.272  10.748
matchDesign                   10.599  0.037  10.641
sesameQC_plotBetaByDesign     10.238  0.167  10.408
visualizeGene                  8.422  0.129   8.554
DMR                            8.191  0.282   8.473
sdf_read_table                 7.230  0.122   7.353
inferStrain                    6.457  0.422   6.881
DML                            6.436  0.240   6.676
estimateLeukocyte              6.475  0.123   6.599
inferTissue                    6.126  0.089   6.216
dyeBiasCorrMostBalanced        6.018  0.105   6.123
getMask                        5.712  0.119   5.832
createUCSCtrack                5.234  0.178   5.413
dyeBiasNL                      5.318  0.092   5.412
deIdentify                     5.289  0.082   5.373
probeSuccessRate               4.908  0.114   5.023
* 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 (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 
 18.866   1.074  19.809 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0010.0000.000
DML6.4360.2406.676
DMLpredict1.2970.0661.363
DMR8.1910.2828.473
ELBAR13.302 0.24913.552
MValueToBetaValue000
SigDF0.3000.0170.316
addMask0.0750.0000.075
betasCollapseToPfx0.0110.0000.011
bisConversionControl4.4380.0684.506
calcEffectSize1.1440.0301.174
checkLevels3.4970.0513.548
cnSegmentation0.2650.0150.280
compareMouseStrainReference11.716 0.12611.845
compareMouseTissueReference000
compareReference10.470 0.27210.748
controls1.9470.0682.015
createUCSCtrack5.2340.1785.413
deIdentify5.2890.0825.373
detectionPnegEcdf0.8570.0050.862
diffRefSet13.475 0.31613.791
dmContrasts1.9170.0291.946
dyeBiasCorr2.5360.1032.639
dyeBiasCorrMostBalanced6.0180.1056.123
dyeBiasL2.7450.0692.814
dyeBiasNL5.3180.0925.412
estimateLeukocyte6.4750.1236.599
formatVCF2.0190.0442.063
getAFTypeIbySumAlleles1.5880.0491.638
getAFs0.9230.0290.952
getBetas0.7070.0200.727
getMask5.7120.1195.832
getRefSet10.934 0.07411.008
imputeBetas16.708 0.44017.152
imputeBetasByGenomicNeighbors33.280 0.57633.859
imputeBetasMatrixByMean0.0010.0000.002
inferEthnicity0.0010.0000.001
inferInfiniumIChannel0.2480.0510.299
inferSex19.277 0.18219.461
inferSpecies12.830 0.61713.447
inferStrain6.4570.4226.881
inferTissue6.1260.0896.216
initFileSet1.1670.0311.199
listAvailableMasks1.2190.0251.245
mLiftOver000
mapFileSet0.0320.0000.033
mapToMammal402.6020.0522.655
matchDesign10.599 0.03710.641
meanIntensity2.5420.0502.593
medianTotalIntensity0.7910.0230.814
noMasked3.3160.0533.369
noob1.9180.0231.941
openSesame4.7610.1254.892
openSesameToFile1.3570.0131.372
pOOBAH1.2530.0001.253
palgen0.0380.0000.037
parseGEOsignalMU2.8850.0852.977
predictAge2.3500.0452.396
predictAgeHorvath3530.0000.0000.001
predictAgeSkinBlood000
predictMouseAgeInMonth0.0000.0000.001
prefixMask0.4240.0110.435
prefixMaskButC0.1280.0010.129
prefixMaskButCG0.0520.0010.052
prepSesame3.4540.0793.533
prepSesameList0.0010.0000.002
print.DMLSummary2.7910.1682.960
print.fileSet1.1230.0321.155
probeID_designType000
probeSuccessRate4.9080.1145.023
qualityMask1.9580.0702.028
reIdentify4.7260.0694.796
readFileSet0.0530.0000.053
readIDATpair0.1030.0040.107
recommendedMaskNames000
resetMask0.3570.0200.377
scrub2.0030.1412.143
scrubSoft3.0300.0483.078
sdfPlatform0.2750.0140.290
sdf_read_table7.2300.1227.353
sdf_write_table1.6860.0621.875
searchIDATprefixes0.0040.0000.005
sesame-package2.2700.0372.310
sesameAnno_attachManifest0.0010.0000.000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges0.0000.0000.001
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats17.730 0.19117.922
sesameQC_getStats1.7420.0031.745
sesameQC_plotBar11.522 0.21611.738
sesameQC_plotBetaByDesign10.238 0.16710.408
sesameQC_plotHeatSNPs16.309 0.23116.541
sesameQC_plotIntensVsBetas1.7220.0351.757
sesameQC_plotRedGrnQQ1.7880.0401.827
sesameQC_rankStats3.1230.0593.182
sesameQCtoDF1.7580.0021.761
sesame_checkVersion0.0040.0000.004
sesamize000
setMask0.080.000.08
signalMU0.7160.0160.732
sliceFileSet0.0330.0000.033
summaryExtractTest2.7730.1052.879
totalIntensities2.3820.0602.443
updateSigDF2.9460.0743.020
visualizeGene8.4220.1298.554
visualizeProbes1.0740.0001.074
visualizeRegion0.3070.0010.307
visualizeSegments1.7370.0291.766