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This page was generated on 2025-10-04 12:07 -0400 (Sat, 04 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 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 12.7.1 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: 2025-10-03 11:34:01 -0000 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 11:48:10 -0000 (Fri, 03 Oct 2025)
EllapsedTime: 848.4 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 43.206  1.095  46.313
inferSex                      26.553  0.446  27.426
imputeBetas                   24.706  0.933  28.500
sesameQC_calcStats            23.513  0.136  24.015
sesameQC_plotHeatSNPs         22.119  0.183  22.689
ELBAR                         17.044  0.143  17.645
compareMouseStrainReference   16.407  0.187  16.958
inferSpecies                  15.993  0.562  17.345
matchDesign                   16.343  0.147  17.576
diffRefSet                    16.193  0.239  16.722
compareReference              13.976  0.172  14.192
sesameQC_plotBetaByDesign     13.185  0.116  13.330
sesameQC_plotBar              13.085  0.184  13.306
getRefSet                     12.542  0.079  13.344
DMR                           11.019  0.258  11.875
visualizeGene                  9.755  0.243  10.036
DML                            9.359  0.367  10.279
inferStrain                    8.514  0.311   9.035
estimateLeukocyte              8.523  0.115   9.525
sdf_read_table                 8.325  0.176   8.520
inferTissue                    7.651  0.136   7.824
dyeBiasCorrMostBalanced        7.140  0.171   7.550
deIdentify                     7.146  0.096   7.284
dyeBiasNL                      6.971  0.072   7.834
getMask                        6.865  0.160   7.342
createUCSCtrack                6.082  0.207   6.311
openSesame                     6.141  0.127   6.992
reIdentify                     5.806  0.068   5.888
probeSuccessRate               5.643  0.100   5.757
bisConversionControl           5.115  0.107   5.389
* 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 
 22.800   1.451  24.854 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML 9.359 0.36710.279
DMLpredict1.5870.0321.678
DMR11.019 0.25811.875
ELBAR17.044 0.14317.645
MValueToBetaValue000
SigDF0.3520.0200.373
addMask0.090.000.09
betasCollapseToPfx0.0160.0000.015
bisConversionControl5.1150.1075.389
calcEffectSize1.3530.0121.385
checkLevels3.3590.1323.507
cnSegmentation0.3440.0080.353
compareMouseStrainReference16.407 0.18716.958
compareMouseTissueReference000
compareReference13.976 0.17214.192
controls2.3360.0322.374
createUCSCtrack6.0820.2076.311
deIdentify7.1460.0967.284
detectionPnegEcdf1.0810.0001.083
diffRefSet16.193 0.23916.722
dmContrasts2.0640.0522.126
dyeBiasCorr3.1470.0953.296
dyeBiasCorrMostBalanced7.1400.1717.550
dyeBiasL3.8600.0924.005
dyeBiasNL6.9710.0727.834
estimateLeukocyte8.5230.1159.525
formatVCF2.3530.0322.394
getAFTypeIbySumAlleles1.8950.0641.967
getAFs1.2320.0161.251
getBetas0.9560.0160.974
getMask6.8650.1607.342
getRefSet12.542 0.07913.344
imputeBetas24.706 0.93328.500
imputeBetasByGenomicNeighbors43.206 1.09546.313
imputeBetasMatrixByMean0.0020.0000.002
inferEthnicity0.0000.0000.001
inferInfiniumIChannel0.2630.1200.383
inferSex26.553 0.44627.426
inferSpecies15.993 0.56217.345
inferStrain8.5140.3119.035
inferTissue7.6510.1367.824
initFileSet1.3040.0361.343
listAvailableMasks1.3330.0161.353
mLiftOver0.0000.0000.001
mapFileSet0.0350.0040.040
mapToMammal402.7280.0782.817
matchDesign16.343 0.14717.576
meanIntensity2.9090.0843.023
medianTotalIntensity0.9790.0321.015
noMasked3.9990.0724.085
noob2.4630.0162.505
openSesame6.1410.1276.992
openSesameToFile1.7820.0121.846
pOOBAH1.4020.0121.426
palgen0.0450.0000.047
parseGEOsignalMU3.0850.0403.138
predictAge2.5730.0242.603
predictAgeHorvath353000
predictAgeSkinBlood0.0010.0000.000
predictMouseAgeInMonth000
prefixMask0.4510.0040.459
prefixMaskButC0.1320.0000.133
prefixMaskButCG0.0580.0000.058
prepSesame4.1250.0324.168
prepSesameList0.0020.0000.002
print.DMLSummary2.8880.1753.072
print.fileSet1.3350.0161.354
probeID_designType000
probeSuccessRate5.6430.1005.757
qualityMask1.9780.0632.047
reIdentify5.8060.0685.888
readFileSet0.0610.0000.061
readIDATpair0.1290.0000.129
recommendedMaskNames000
resetMask0.4520.0240.477
scrub2.9550.0723.071
scrubSoft4.2470.0164.274
sdfPlatform0.3540.0280.383
sdf_read_table8.3250.1768.520
sdf_write_table2.3120.0632.566
searchIDATprefixes0.0060.0000.009
sesame-package2.5650.0602.631
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats23.513 0.13624.015
sesameQC_getStats2.1690.0042.176
sesameQC_plotBar13.085 0.18413.306
sesameQC_plotBetaByDesign13.185 0.11613.330
sesameQC_plotHeatSNPs22.119 0.18322.689
sesameQC_plotIntensVsBetas2.3030.0202.330
sesameQC_plotRedGrnQQ1.5460.0281.578
sesameQC_rankStats4.1560.1314.716
sesameQCtoDF1.8920.0201.919
sesame_checkVersion0.0050.0000.004
sesamize0.0010.0000.000
setMask0.1030.0040.109
signalMU0.9460.0280.978
sliceFileSet0.0390.0000.039
summaryExtractTest3.1950.1633.369
totalIntensities2.7360.0762.822
updateSigDF3.5320.1513.698
visualizeGene 9.755 0.24310.036
visualizeProbes1.6060.0241.636
visualizeRegion0.4590.0000.460
visualizeSegments1.8220.0591.911