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This page was generated on 2025-09-29 12:07 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4833
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4621
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4566
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 1969/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-09-28 13:45 -0400 (Sun, 28 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: sesame
Version: 1.27.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sesame_1.27.1.tar.gz
StartedAt: 2025-09-26 12:09:20 -0000 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 12:25:57 -0000 (Fri, 26 Sep 2025)
EllapsedTime: 996.8 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sesame_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/sesame.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 41.464  0.624  53.425
inferSex                      26.765  0.313  36.608
imputeBetas                   25.507  0.758  32.792
sesameQC_plotHeatSNPs         23.836  0.239  27.044
sesameQC_calcStats            22.628  0.136  25.762
inferSpecies                  18.971  0.510  24.274
ELBAR                         17.275  0.203  20.124
compareMouseStrainReference   16.823  0.265  22.849
matchDesign                   16.301  0.086  21.568
diffRefSet                    15.027  0.247  17.991
compareReference              14.024  0.151  18.008
sesameQC_plotBetaByDesign     13.588  0.084  17.221
getRefSet                     13.276  0.199  16.348
sesameQC_plotBar              13.168  0.233  14.120
DMR                           10.717  0.302  13.844
visualizeGene                  9.654  0.279  14.183
DML                            9.320  0.343  12.484
inferStrain                    9.091  0.262  11.989
sdf_read_table                 8.367  0.156   9.987
inferTissue                    7.907  0.064  10.915
dyeBiasNL                      7.618  0.082   8.731
deIdentify                     7.342  0.064   7.867
estimateLeukocyte              7.249  0.150   9.224
getMask                        6.850  0.167   8.333
dyeBiasCorrMostBalanced        6.801  0.191   7.402
createUCSCtrack                6.258  0.132   6.748
openSesame                     6.052  0.083   7.000
reIdentify                     6.039  0.080   6.507
probeSuccessRate               5.677  0.083   6.644
bisConversionControl           4.965  0.072   5.494
sesameQC_rankStats             4.457  0.075   5.807
prepSesame                     4.289  0.036   6.418
noMasked                       4.119  0.111   5.107
updateSigDF                    3.724  0.115   5.716
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

sesame.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
 21.467   0.789  26.245 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0010.0000.000
DML 9.320 0.34312.484
DMLpredict1.4620.0401.518
DMR10.717 0.30213.844
ELBAR17.275 0.20320.124
MValueToBetaValue000
SigDF0.3500.0240.751
addMask0.0910.0040.192
betasCollapseToPfx0.0170.0000.035
bisConversionControl4.9650.0725.494
calcEffectSize1.3530.0281.537
checkLevels3.3470.0844.532
cnSegmentation0.3380.0320.374
compareMouseStrainReference16.823 0.26522.849
compareMouseTissueReference000
compareReference14.024 0.15118.008
controls2.2290.0552.306
createUCSCtrack6.2580.1326.748
deIdentify7.3420.0647.867
detectionPnegEcdf1.0540.0071.577
diffRefSet15.027 0.24717.991
dmContrasts1.9700.0432.062
dyeBiasCorr3.0680.0363.393
dyeBiasCorrMostBalanced6.8010.1917.402
dyeBiasL2.5390.0392.741
dyeBiasNL7.6180.0828.731
estimateLeukocyte7.2490.1509.224
formatVCF2.3000.0402.857
getAFTypeIbySumAlleles1.8970.0552.413
getAFs1.3390.0201.450
getBetas1.0220.0081.033
getMask6.8500.1678.333
getRefSet13.276 0.19916.348
imputeBetas25.507 0.75832.792
imputeBetasByGenomicNeighbors41.464 0.62453.425
imputeBetasMatrixByMean0.0020.0000.002
inferEthnicity0.0010.0000.001
inferInfiniumIChannel0.2890.1000.655
inferSex26.765 0.31336.608
inferSpecies18.971 0.51024.274
inferStrain 9.091 0.26211.989
inferTissue 7.907 0.06410.915
initFileSet1.3430.0322.271
listAvailableMasks1.3950.0231.686
mLiftOver000
mapFileSet0.0410.0000.042
mapToMammal402.7340.0403.175
matchDesign16.301 0.08621.568
meanIntensity3.0000.1153.392
medianTotalIntensity1.0000.0361.043
noMasked4.1190.1115.107
noob2.4960.0112.705
openSesame6.0520.0837.000
openSesameToFile1.8430.0161.996
pOOBAH1.4280.0001.518
palgen0.0420.0040.061
parseGEOsignalMU3.1670.0844.603
predictAge2.6200.0393.190
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth0.0000.0000.001
prefixMask0.5390.0000.545
prefixMaskButC0.1590.0000.206
prefixMaskButCG0.0680.0000.137
prepSesame4.2890.0366.418
prepSesameList0.0010.0000.001
print.DMLSummary3.0020.1433.430
print.fileSet1.3120.0321.632
probeID_designType000
probeSuccessRate5.6770.0836.644
qualityMask1.9790.0592.662
reIdentify6.0390.0806.507
readFileSet0.0510.0040.057
readIDATpair0.1370.0030.139
recommendedMaskNames000
resetMask0.4670.0280.496
scrub2.9000.0673.245
scrubSoft4.4350.0644.946
sdfPlatform0.3270.0390.368
sdf_read_table8.3670.1569.987
sdf_write_table2.3520.0593.228
searchIDATprefixes0.0050.0000.020
sesame-package2.6050.0562.742
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download0.0000.0000.001
sesameAnno_readManifestTSV000
sesameQC_calcStats22.628 0.13625.762
sesameQC_getStats2.2510.0042.270
sesameQC_plotBar13.168 0.23314.120
sesameQC_plotBetaByDesign13.588 0.08417.221
sesameQC_plotHeatSNPs23.836 0.23927.044
sesameQC_plotIntensVsBetas2.4470.0362.967
sesameQC_plotRedGrnQQ1.5720.0283.207
sesameQC_rankStats4.4570.0755.807
sesameQCtoDF1.9870.0032.054
sesame_checkVersion0.0040.0000.004
sesamize0.0010.0000.007
setMask0.1210.0000.141
signalMU1.2380.0081.271
sliceFileSet0.0400.0010.041
summaryExtractTest3.0250.0473.244
totalIntensities2.9320.0803.866
updateSigDF3.7240.1155.716
visualizeGene 9.654 0.27914.183
visualizeProbes1.5960.0121.926
visualizeRegion0.4530.0000.548
visualizeSegments1.7720.1191.985