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This page was generated on 2025-09-22 12:07 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 1968/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.27.1  (landing page)
Wanding Zhou
Snapshot Date: 2025-09-21 13:45 -0400 (Sun, 21 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: 2025-09-19 13:22:03 -0000 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 13:40:07 -0000 (Fri, 19 Sep 2025)
EllapsedTime: 1083.4 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 39.573  0.511  55.278
imputeBetas                   24.329  0.434  40.930
inferSex                      23.387  0.188  31.861
sesameQC_calcStats            21.551  0.084  34.283
sesameQC_plotHeatSNPs         20.771  0.231  24.512
inferSpecies                  16.903  0.650  20.049
matchDesign                   15.877  0.152  19.293
compareMouseStrainReference   15.679  0.218  20.399
ELBAR                         15.040  0.183  20.303
diffRefSet                    14.649  0.294  20.611
compareReference              13.643  0.159  16.170
getRefSet                     12.446  0.155  19.206
sesameQC_plotBar              12.230  0.192  18.823
sesameQC_plotBetaByDesign     12.122  0.104  16.768
DMR                           10.031  0.199  16.896
visualizeGene                  8.895  0.172  11.646
DML                            8.582  0.288  11.535
inferStrain                    8.447  0.328  11.910
sdf_read_table                 8.045  0.171   9.741
inferTissue                    7.278  0.100  10.551
dyeBiasNL                      7.039  0.080   9.524
deIdentify                     6.940  0.064   9.744
estimateLeukocyte              6.802  0.098  10.373
dyeBiasCorrMostBalanced        6.620  0.169   7.840
getMask                        6.426  0.176   8.574
createUCSCtrack                5.961  0.127   9.461
reIdentify                     5.868  0.060   6.479
openSesame                     5.798  0.088   7.325
probeSuccessRate               5.261  0.128   6.404
bisConversionControl           4.599  0.084   6.769
scrubSoft                      4.268  0.016   6.036
sesameQC_rankStats             3.959  0.076   5.998
prepSesame                     3.975  0.048   6.506
noMasked                       3.834  0.079   6.281
* 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 
 20.345   0.795  25.560 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0010.0000.000
DML 8.582 0.28811.535
DMLpredict1.4750.0361.597
DMR10.031 0.19916.896
ELBAR15.040 0.18320.303
MValueToBetaValue0.0000.0000.001
SigDF0.3300.0080.375
addMask0.070.000.07
betasCollapseToPfx0.0150.0000.015
bisConversionControl4.5990.0846.769
calcEffectSize1.2520.0321.287
checkLevels3.1250.0804.970
cnSegmentation0.3300.0080.339
compareMouseStrainReference15.679 0.21820.399
compareMouseTissueReference000
compareReference13.643 0.15916.170
controls2.1830.0672.707
createUCSCtrack5.9610.1279.461
deIdentify6.9400.0649.744
detectionPnegEcdf1.0010.0001.147
diffRefSet14.649 0.29420.611
dmContrasts1.9420.0282.745
dyeBiasCorr2.9850.0363.600
dyeBiasCorrMostBalanced6.6200.1697.840
dyeBiasL2.3330.0762.453
dyeBiasNL7.0390.0809.524
estimateLeukocyte 6.802 0.09810.373
formatVCF2.2090.0523.596
getAFTypeIbySumAlleles1.8810.0573.598
getAFs1.2630.0041.510
getBetas0.9160.0160.978
getMask6.4260.1768.574
getRefSet12.446 0.15519.206
imputeBetas24.329 0.43440.930
imputeBetasByGenomicNeighbors39.573 0.51155.278
imputeBetasMatrixByMean0.0020.0000.001
inferEthnicity0.0000.0000.001
inferInfiniumIChannel0.2670.0990.492
inferSex23.387 0.18831.861
inferSpecies16.903 0.65020.049
inferStrain 8.447 0.32811.910
inferTissue 7.278 0.10010.551
initFileSet1.2520.0402.058
listAvailableMasks1.3470.0321.397
mLiftOver0.0010.0000.000
mapFileSet0.0410.0000.040
mapToMammal402.7320.0484.401
matchDesign15.877 0.15219.293
meanIntensity2.7900.0842.916
medianTotalIntensity0.9520.0161.790
noMasked3.8340.0796.281
noob2.3530.0002.824
openSesame5.7980.0887.325
openSesameToFile1.8050.0042.761
pOOBAH1.4170.0042.854
palgen0.0390.0080.100
parseGEOsignalMU3.0950.0764.841
predictAge2.5530.0193.065
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.5050.0030.510
prefixMaskButC0.1510.0000.152
prefixMaskButCG0.0630.0040.067
prepSesame3.9750.0486.506
prepSesameList0.0010.0000.006
print.DMLSummary2.6950.0993.290
print.fileSet1.2420.0361.314
probeID_designType000
probeSuccessRate5.2610.1286.404
qualityMask1.9900.0482.760
reIdentify5.8680.0606.479
readFileSet0.0540.0040.059
readIDATpair0.1140.0000.115
recommendedMaskNames0.0000.0000.001
resetMask0.3920.0270.421
scrub2.7500.0642.917
scrubSoft4.2680.0166.036
sdfPlatform0.3250.0400.382
sdf_read_table8.0450.1719.741
sdf_write_table2.2910.0642.773
searchIDATprefixes0.0050.0000.028
sesame-package2.4470.0682.630
sesameAnno_attachManifest000
sesameAnno_buildAddressFile0.0010.0000.000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats21.551 0.08434.283
sesameQC_getStats2.1020.0082.617
sesameQC_plotBar12.230 0.19218.823
sesameQC_plotBetaByDesign12.122 0.10416.768
sesameQC_plotHeatSNPs20.771 0.23124.512
sesameQC_plotIntensVsBetas2.1250.0402.787
sesameQC_plotRedGrnQQ1.4530.0522.063
sesameQC_rankStats3.9590.0765.998
sesameQCtoDF1.9060.0001.940
sesame_checkVersion0.0040.0000.004
sesamize000
setMask0.0930.0000.093
signalMU1.0380.0241.082
sliceFileSet0.0360.0000.036
summaryExtractTest2.7350.0403.825
totalIntensities2.5360.0473.089
updateSigDF3.3100.1404.437
visualizeGene 8.895 0.17211.646
visualizeProbes1.4310.0001.437
visualizeRegion0.4230.0080.431
visualizeSegments1.5070.0991.621