Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-09-15 12:03 -0400 (Mon, 15 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4719
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4538
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4522
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4543
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 1964/2327HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-09-14 13:45 -0400 (Sun, 14 Sep 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: 2025-09-15 03:55:13 -0400 (Mon, 15 Sep 2025)
EndedAt: 2025-09-15 04:13:24 -0400 (Mon, 15 Sep 2025)
EllapsedTime: 1091.2 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 33.182  0.571  33.756
inferSex                      20.544  0.065  20.611
ELBAR                         19.582  0.161  19.782
sesameQC_calcStats            18.761  0.052  18.815
sesameQC_plotHeatSNPs         16.874  0.216  17.093
compareReference              15.745  0.405  16.151
imputeBetas                   15.592  0.500  16.093
inferSpecies                  14.758  0.671  15.430
diffRefSet                    13.810  0.317  14.129
compareMouseStrainReference   13.206  0.236  13.443
sesameQC_plotBar              12.285  0.197  12.482
getRefSet                     11.191  0.068  11.261
matchDesign                   11.005  0.061  11.072
DMR                           10.174  0.248  10.496
DML                            9.387  0.419   9.807
createUCSCtrack                9.369  0.148   9.518
sesameQC_plotBetaByDesign      9.038  0.081   9.122
visualizeGene                  8.552  0.093   8.646
sdf_read_table                 7.020  0.107   7.127
inferStrain                    6.528  0.405   6.936
dyeBiasCorrMostBalanced        6.387  0.090   6.477
estimateLeukocyte              6.343  0.101   6.452
dyeBiasNL                      6.111  0.074   6.188
inferTissue                    5.871  0.189   6.060
bisConversionControl           5.957  0.069   6.029
deIdentify                     5.928  0.094   6.023
getMask                        5.536  0.102   5.641
probeSuccessRate               5.013  0.107   5.120
openSesame                     4.966  0.116   5.090
* 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

##############################################################################
##############################################################################
###
### 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 
 18.638   0.983  19.608 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML9.3870.4199.807
DMLpredict1.5860.0481.634
DMR10.174 0.24810.496
ELBAR19.582 0.16119.782
MValueToBetaValue000
SigDF0.3300.0130.351
addMask0.1860.0050.192
betasCollapseToPfx0.0130.0000.013
bisConversionControl5.9570.0696.029
calcEffectSize2.2100.0512.277
checkLevels4.5630.0754.676
cnSegmentation0.4750.0150.490
compareMouseStrainReference13.206 0.23613.443
compareMouseTissueReference000
compareReference15.745 0.40516.151
controls3.4900.0613.551
createUCSCtrack9.3690.1489.518
deIdentify5.9280.0946.023
detectionPnegEcdf0.9500.0110.961
diffRefSet13.810 0.31714.129
dmContrasts1.7860.0341.821
dyeBiasCorr2.4830.0762.559
dyeBiasCorrMostBalanced6.3870.0906.477
dyeBiasL2.2920.0762.368
dyeBiasNL6.1110.0746.188
estimateLeukocyte6.3430.1016.452
formatVCF1.9410.0491.990
getAFTypeIbySumAlleles1.5520.0291.581
getAFs0.9590.0190.978
getBetas0.7550.0150.769
getMask5.5360.1025.641
getRefSet11.191 0.06811.261
imputeBetas15.592 0.50016.093
imputeBetasByGenomicNeighbors33.182 0.57133.756
imputeBetasMatrixByMean0.0010.0000.001
inferEthnicity000
inferInfiniumIChannel0.2270.0640.291
inferSex20.544 0.06520.611
inferSpecies14.758 0.67115.430
inferStrain6.5280.4056.936
inferTissue5.8710.1896.060
initFileSet1.0910.0241.114
listAvailableMasks1.1970.0211.218
mLiftOver0.0000.0000.001
mapFileSet0.0320.0010.033
mapToMammal402.3380.0432.381
matchDesign11.005 0.06111.072
meanIntensity2.5170.0472.564
medianTotalIntensity0.8150.0170.832
noMasked3.5000.0593.559
noob1.8370.0001.837
openSesame4.9660.1165.090
openSesameToFile1.4240.0391.465
pOOBAH1.2350.0101.245
palgen0.0360.0010.036
parseGEOsignalMU2.8570.0582.915
predictAge2.5230.0652.587
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.4050.0010.407
prefixMaskButC0.1120.0010.113
prefixMaskButCG0.0470.0000.047
prepSesame3.5850.0793.666
prepSesameList0.0010.0000.001
print.DMLSummary2.8250.1372.961
print.fileSet1.1460.0371.183
probeID_designType000
probeSuccessRate5.0130.1075.120
qualityMask1.7230.0411.763
reIdentify4.4820.0514.533
readFileSet0.0510.0000.051
readIDATpair0.1020.0010.104
recommendedMaskNames000
resetMask0.3730.0090.383
scrub2.2210.1882.409
scrubSoft3.0260.0293.056
sdfPlatform0.2690.0120.281
sdf_read_table7.0200.1077.127
sdf_write_table1.6520.0441.817
searchIDATprefixes0.0030.0000.005
sesame-package2.0550.0292.085
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats18.761 0.05218.815
sesameQC_getStats1.880.001.88
sesameQC_plotBar12.285 0.19712.482
sesameQC_plotBetaByDesign9.0380.0819.122
sesameQC_plotHeatSNPs16.874 0.21617.093
sesameQC_plotIntensVsBetas1.8770.0201.897
sesameQC_plotRedGrnQQ1.8120.0331.845
sesameQC_rankStats2.9750.0693.044
sesameQCtoDF1.7590.0201.779
sesame_checkVersion0.0030.0000.003
sesamize0.0010.0000.000
setMask0.0960.0010.097
signalMU0.7950.0130.808
sliceFileSet0.0330.0020.034
summaryExtractTest2.450.102.55
totalIntensities2.2550.0622.317
updateSigDF2.8850.0912.977
visualizeGene8.5520.0938.646
visualizeProbes1.1340.0041.139
visualizeRegion0.3180.0000.318
visualizeSegments1.7770.0191.797