| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-17 11:35 -0500 (Wed, 17 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4589 |
| 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 1966/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sesame 1.29.0 (landing page) Wanding Zhou
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
|
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. |
| Package: sesame |
| Version: 1.29.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sesame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sesame_1.29.0.tar.gz |
| StartedAt: 2025-12-16 22:10:43 -0500 (Tue, 16 Dec 2025) |
| EndedAt: 2025-12-16 22:15:57 -0500 (Tue, 16 Dec 2025) |
| EllapsedTime: 314.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sesame.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sesame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sesame_1.29.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/sesame.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.29.0’
* 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 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 15.101 0.622 16.469
inferSex 9.624 0.495 10.651
sesameQC_calcStats 8.400 0.911 9.992
sesameQC_plotHeatSNPs 8.021 0.868 9.369
imputeBetas 7.705 0.723 8.999
ELBAR 5.956 1.394 7.810
sesameQC_plotBar 6.978 0.215 7.652
inferSpecies 6.815 0.377 7.575
diffRefSet 6.020 0.249 6.666
getRefSet 6.000 0.214 6.567
matchDesign 4.657 0.276 5.094
* 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
sesame.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sesame ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘sesame’ ... ** this is package ‘sesame’ version ‘1.29.0’ ** 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)
sesame.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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
8.205 0.311 9.045
sesame.Rcheck/sesame-Ex.timings
| name | user | system | elapsed | |
| BetaValueToMValue | 0 | 0 | 0 | |
| DML | 2.330 | 0.089 | 2.614 | |
| DMLpredict | 0.418 | 0.039 | 0.496 | |
| DMR | 3.296 | 0.089 | 3.626 | |
| ELBAR | 5.956 | 1.394 | 7.810 | |
| MValueToBetaValue | 0 | 0 | 0 | |
| SigDF | 0.096 | 0.021 | 0.132 | |
| addMask | 0.046 | 0.013 | 0.069 | |
| betasCollapseToPfx | 0.004 | 0.000 | 0.005 | |
| bisConversionControl | 2.202 | 0.075 | 2.450 | |
| calcEffectSize | 0.419 | 0.046 | 0.496 | |
| checkLevels | 1.698 | 0.076 | 1.885 | |
| cnSegmentation | 0.088 | 0.021 | 0.116 | |
| compareMouseStrainReference | 4.066 | 0.213 | 4.445 | |
| compareMouseTissueReference | 0.000 | 0.001 | 0.000 | |
| compareReference | 4.611 | 0.236 | 4.974 | |
| controls | 0.766 | 0.092 | 0.898 | |
| createUCSCtrack | 2.301 | 0.159 | 2.610 | |
| deIdentify | 2.135 | 0.182 | 2.407 | |
| detectionPnegEcdf | 0.432 | 0.012 | 0.464 | |
| diffRefSet | 6.020 | 0.249 | 6.666 | |
| dmContrasts | 0.742 | 0.094 | 0.901 | |
| dyeBiasCorr | 1.058 | 0.113 | 1.247 | |
| dyeBiasCorrMostBalanced | 3.425 | 0.127 | 3.752 | |
| dyeBiasL | 1.003 | 0.091 | 1.198 | |
| dyeBiasNL | 2.015 | 0.200 | 2.347 | |
| estimateLeukocyte | 2.847 | 0.201 | 3.237 | |
| formatVCF | 0.804 | 0.111 | 0.984 | |
| getAFTypeIbySumAlleles | 0.572 | 0.085 | 0.725 | |
| getAFs | 0.399 | 0.065 | 0.509 | |
| getBetas | 0.284 | 0.041 | 0.358 | |
| getMask | 2.749 | 0.269 | 3.237 | |
| getRefSet | 6.000 | 0.214 | 6.567 | |
| imputeBetas | 7.705 | 0.723 | 8.999 | |
| imputeBetasByGenomicNeighbors | 15.101 | 0.622 | 16.469 | |
| imputeBetasMatrixByMean | 0.001 | 0.000 | 0.001 | |
| inferEthnicity | 0 | 0 | 0 | |
| inferInfiniumIChannel | 0.150 | 0.238 | 0.404 | |
| inferSex | 9.624 | 0.495 | 10.651 | |
| inferSpecies | 6.815 | 0.377 | 7.575 | |
| inferStrain | 3.601 | 0.228 | 4.079 | |
| inferTissue | 2.378 | 0.319 | 2.828 | |
| initFileSet | 0.364 | 0.080 | 0.464 | |
| listAvailableMasks | 0.394 | 0.060 | 0.464 | |
| mLiftOver | 0.000 | 0.001 | 0.000 | |
| mapFileSet | 0.016 | 0.001 | 0.017 | |
| mapToMammal40 | 0.849 | 0.138 | 1.018 | |
| matchDesign | 4.657 | 0.276 | 5.094 | |
| meanIntensity | 0.995 | 0.128 | 1.158 | |
| medianTotalIntensity | 0.302 | 0.046 | 0.357 | |
| noMasked | 1.291 | 0.087 | 1.419 | |
| noob | 0.831 | 0.105 | 0.948 | |
| openSesame | 1.842 | 0.294 | 2.206 | |
| openSesameToFile | 0.603 | 0.068 | 0.685 | |
| pOOBAH | 0.541 | 0.023 | 0.574 | |
| palgen | 0.018 | 0.003 | 0.021 | |
| parseGEOsignalMU | 1.326 | 0.097 | 1.482 | |
| predictAge | 1.140 | 0.080 | 1.263 | |
| predictAgeHorvath353 | 0 | 0 | 0 | |
| predictAgeSkinBlood | 0 | 0 | 0 | |
| predictMouseAgeInMonth | 0.000 | 0.001 | 0.000 | |
| prefixMask | 0.232 | 0.002 | 0.237 | |
| prefixMaskButC | 0.055 | 0.001 | 0.056 | |
| prefixMaskButCG | 0.025 | 0.001 | 0.026 | |
| prepSesame | 1.308 | 0.125 | 1.514 | |
| prepSesameList | 0.001 | 0.001 | 0.001 | |
| print.DMLSummary | 1.439 | 0.213 | 1.757 | |
| print.fileSet | 0.376 | 0.057 | 0.481 | |
| probeID_designType | 0 | 0 | 0 | |
| probeSuccessRate | 2.354 | 0.229 | 2.757 | |
| qualityMask | 0.785 | 0.110 | 0.918 | |
| reIdentify | 1.832 | 0.086 | 2.004 | |
| readFileSet | 0.035 | 0.003 | 0.038 | |
| readIDATpair | 0.065 | 0.005 | 0.071 | |
| recommendedMaskNames | 0.000 | 0.001 | 0.000 | |
| resetMask | 0.137 | 0.029 | 0.177 | |
| scrub | 1.016 | 0.166 | 1.257 | |
| scrubSoft | 1.453 | 0.377 | 1.927 | |
| sdfPlatform | 0.092 | 0.020 | 0.124 | |
| sdf_read_table | 3.908 | 0.221 | 4.276 | |
| sdf_write_table | 1.059 | 0.074 | 1.182 | |
| searchIDATprefixes | 0.001 | 0.002 | 0.004 | |
| sesame-package | 0.924 | 0.086 | 1.054 | |
| sesameAnno_attachManifest | 0.000 | 0.000 | 0.001 | |
| sesameAnno_buildAddressFile | 0 | 0 | 0 | |
| sesameAnno_buildManifestGRanges | 0.001 | 0.001 | 0.000 | |
| sesameAnno_download | 0.000 | 0.000 | 0.001 | |
| sesameAnno_readManifestTSV | 0 | 0 | 0 | |
| sesameQC_calcStats | 8.400 | 0.911 | 9.992 | |
| sesameQC_getStats | 0.863 | 0.033 | 0.946 | |
| sesameQC_plotBar | 6.978 | 0.215 | 7.652 | |
| sesameQC_plotBetaByDesign | 3.701 | 0.537 | 4.472 | |
| sesameQC_plotHeatSNPs | 8.021 | 0.868 | 9.369 | |
| sesameQC_plotIntensVsBetas | 0.583 | 0.122 | 0.737 | |
| sesameQC_plotRedGrnQQ | 0.564 | 0.134 | 0.739 | |
| sesameQC_rankStats | 1.032 | 0.150 | 1.244 | |
| sesameQCtoDF | 0.930 | 0.057 | 1.028 | |
| sesame_checkVersion | 0.001 | 0.001 | 0.001 | |
| sesamize | 0 | 0 | 0 | |
| setMask | 0.026 | 0.002 | 0.029 | |
| signalMU | 0.273 | 0.035 | 0.317 | |
| sliceFileSet | 0.016 | 0.002 | 0.017 | |
| summaryExtractTest | 1.347 | 0.175 | 1.577 | |
| totalIntensities | 0.902 | 0.101 | 1.030 | |
| updateSigDF | 1.090 | 0.145 | 1.309 | |
| visualizeGene | 3.778 | 0.227 | 4.101 | |
| visualizeProbes | 0.468 | 0.015 | 0.488 | |
| visualizeRegion | 0.119 | 0.006 | 0.125 | |
| visualizeSegments | 0.892 | 0.078 | 1.035 | |