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This page was generated on 2025-10-02 11:42 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4831
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4612
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4584
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 1.26.0  (landing page)
Wanding Zhou
Snapshot Date: 2025-09-29 13:40 -0400 (Mon, 29 Sep 2025)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_21
git_last_commit: bc933e0
git_last_commit_date: 2025-04-15 11:34:53 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for sesame on kunpeng2

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: 1.26.0
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_1.26.0.tar.gz
StartedAt: 2025-09-30 14:35:51 -0000 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 14:50:39 -0000 (Tue, 30 Sep 2025)
EllapsedTime: 888.1 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/sesame.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.26.0’
* 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 45.550  0.534  46.222
sesameQC_calcStats            29.819  0.203  30.110
inferSex                      28.226  0.283  28.599
imputeBetas                   27.563  0.476  30.358
sesameQC_plotHeatSNPs         27.046  0.276  27.387
ELBAR                         23.112  0.128  23.282
sesameQC_plotBetaByDesign     19.208  0.100  19.352
inferSpecies                  18.489  0.423  18.948
compareMouseStrainReference   17.807  0.104  17.951
matchDesign                   16.982  0.140  17.192
diffRefSet                    16.613  0.192  16.840
compareReference              15.603  0.236  15.873
sesameQC_plotBar              13.200  0.187  13.455
getRefSet                     13.239  0.108  13.367
DMR                           11.172  0.235  11.435
inferStrain                   10.138  0.359  10.526
visualizeGene                  9.813  0.175  10.007
DML                            9.136  0.247   9.413
inferTissue                    9.023  0.151   9.220
sdf_read_table                 8.882  0.124   9.020
estimateLeukocyte              8.775  0.116   8.921
dyeBiasNL                      8.283  0.068   8.386
deidentify                     8.086  0.071   8.179
reIdentify                     6.900  0.096   7.007
dyeBiasCorrMostBalanced        6.796  0.099   6.962
getMask                        6.697  0.147   6.864
openSesame                     6.521  0.076   6.638
scrubSoft                      6.407  0.048   6.463
probeSuccessRate               6.172  0.112   6.295
createUCSCtrack                6.144  0.132   6.289
prepSesame                     5.305  0.063   5.383
sesameQC_rankStats             5.179  0.076   5.265
bisConversionControl           4.958  0.088   5.060
* 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-devel_2025-02-19/site-library’
* installing *source* package ‘sesame’ ...
** this is package ‘sesame’ version ‘1.26.0’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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 
 23.515   0.832  24.372 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML9.1360.2479.413
DMLpredict1.5340.0481.586
DMR11.172 0.23511.435
ELBAR23.112 0.12823.282
MValueToBetaValue000
SigDF0.3700.0160.388
addMask0.1220.0000.122
betasCollapseToPfx0.0160.0000.017
bisConversionControl4.9580.0885.060
calcEffectSize1.3740.0361.413
checkLevels3.5980.0433.651
cnSegmentation0.3490.0110.361
compareMouseStrainReference17.807 0.10417.951
compareMouseTissueReference000
compareReference15.603 0.23615.873
controls2.2800.0402.324
createUCSCtrack6.1440.1326.289
deidentify8.0860.0718.179
detectionPnegEcdf1.2380.0121.252
diffRefSet16.613 0.19216.840
dmContrasts2.2690.0482.321
dyeBiasCorr3.4590.0603.525
dyeBiasCorrMostBalanced6.7960.0996.962
dyeBiasL2.9740.0563.035
dyeBiasNL8.2830.0688.386
estimateLeukocyte8.7750.1168.921
formatVCF2.4360.0762.517
getAFTypeIbySumAlleles2.1200.0442.183
getAFs1.4460.0281.477
getBetas1.1820.0281.212
getMask6.6970.1476.864
getRefSet13.239 0.10813.367
imputeBetas27.563 0.47630.358
imputeBetasByGenomicNeighbors45.550 0.53446.222
imputeBetasMatrixByMean0.0010.0010.002
inferEthnicity0.0010.0000.001
inferInfiniumIChannel0.3570.0910.450
inferSex28.226 0.28328.599
inferSpecies18.489 0.42318.948
inferStrain10.138 0.35910.526
inferTissue9.0230.1519.220
initFileSet1.3240.0321.360
listAvailableMasks1.5120.0241.539
mLiftOver0.0000.0000.001
mapFileSet0.0380.0000.039
mapToMammal403.3430.0843.439
matchDesign16.982 0.14017.192
meanIntensity3.1810.1193.312
medianTotalIntensity1.3070.0201.330
noMasked4.4230.1124.543
noob3.7160.0763.798
openSesame6.5210.0766.638
openSesameToFile2.1310.0202.161
pOOBAH1.7500.0001.752
palgen0.0480.0000.049
parseGEOsignalMU3.5300.0523.590
predictAge2.4650.0522.521
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.490.000.49
prefixMaskButC0.1430.0000.143
prefixMaskButCG0.0620.0000.062
prepSesame5.3050.0635.383
prepSesameList0.0020.0000.001
print.DMLSummary3.2090.1323.346
print.fileSet1.3240.0321.363
probeID_designType0.0010.0000.000
probeSuccessRate6.1720.1126.295
qualityMask2.3900.0722.466
reIdentify6.9000.0967.007
readFileSet0.0580.0000.059
readIDATpair0.1410.0080.148
recommendedMaskNames000
resetMask0.4710.0200.492
scrub4.0700.0484.123
scrubSoft6.4070.0486.463
sdfPlatform0.3690.0190.390
sdf_read_table8.8820.1249.020
sdf_write_table2.2930.0722.454
searchIDATprefixes0.0060.0000.011
sesame-package3.1060.0883.204
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats29.819 0.20330.110
sesameQC_getStats2.4150.0002.419
sesameQC_plotBar13.200 0.18713.455
sesameQC_plotBetaByDesign19.208 0.10019.352
sesameQC_plotHeatSNPs27.046 0.27627.387
sesameQC_plotIntensVsBetas3.3580.0483.412
sesameQC_plotRedGrnQQ1.8930.0591.955
sesameQC_rankStats5.1790.0765.265
sesameQCtoDF2.5360.0082.546
sesame_checkVersion0.0050.0000.004
sesamize000
setMask0.1450.0000.145
signalMU1.1990.0201.220
sliceFileSet0.0420.0000.043
summaryExtractTest3.1110.1673.284
totalIntensities2.9210.0642.989
updateSigDF3.6360.1363.778
visualizeGene 9.813 0.17510.007
visualizeProbes1.6020.0121.616
visualizeRegion0.4750.0000.476
visualizeSegments1.9710.0241.998