| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-16 11:35 -0500 (Tue, 16 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" | 4583 |
| 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: 2025-12-15 22:10:47 -0500 (Mon, 15 Dec 2025) |
| EndedAt: 2025-12-15 22:15:59 -0500 (Mon, 15 Dec 2025) |
| EllapsedTime: 312.0 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
###
##############################################################################
##############################################################################
* 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 14.851 0.651 16.293
inferSex 9.480 0.547 10.476
sesameQC_calcStats 8.417 0.850 9.816
sesameQC_plotHeatSNPs 8.114 0.871 9.429
imputeBetas 7.708 0.725 9.054
ELBAR 5.877 1.391 7.788
inferSpecies 6.805 0.352 7.454
sesameQC_plotBar 6.899 0.217 7.569
diffRefSet 6.066 0.248 6.704
getRefSet 5.958 0.209 6.579
compareReference 4.707 0.209 5.054
matchDesign 4.603 0.301 5.088
* 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
8.063 0.297 8.812
sesame.Rcheck/sesame-Ex.timings
| name | user | system | elapsed | |
| BetaValueToMValue | 0 | 0 | 0 | |
| DML | 2.316 | 0.096 | 2.527 | |
| DMLpredict | 0.413 | 0.041 | 0.467 | |
| DMR | 3.288 | 0.093 | 3.596 | |
| ELBAR | 5.877 | 1.391 | 7.788 | |
| MValueToBetaValue | 0 | 0 | 0 | |
| SigDF | 0.094 | 0.015 | 0.110 | |
| addMask | 0.043 | 0.012 | 0.060 | |
| betasCollapseToPfx | 0.006 | 0.001 | 0.005 | |
| bisConversionControl | 2.259 | 0.093 | 2.462 | |
| calcEffectSize | 0.416 | 0.059 | 0.515 | |
| checkLevels | 1.661 | 0.082 | 1.874 | |
| cnSegmentation | 0.090 | 0.019 | 0.123 | |
| compareMouseStrainReference | 4.044 | 0.150 | 4.387 | |
| compareMouseTissueReference | 0 | 0 | 0 | |
| compareReference | 4.707 | 0.209 | 5.054 | |
| controls | 0.767 | 0.066 | 0.873 | |
| createUCSCtrack | 2.258 | 0.137 | 2.502 | |
| deIdentify | 2.091 | 0.156 | 2.344 | |
| detectionPnegEcdf | 0.424 | 0.011 | 0.449 | |
| diffRefSet | 6.066 | 0.248 | 6.704 | |
| dmContrasts | 0.782 | 0.090 | 0.967 | |
| dyeBiasCorr | 1.057 | 0.101 | 1.227 | |
| dyeBiasCorrMostBalanced | 3.446 | 0.134 | 3.804 | |
| dyeBiasL | 0.970 | 0.069 | 1.081 | |
| dyeBiasNL | 2.030 | 0.248 | 2.486 | |
| estimateLeukocyte | 2.796 | 0.187 | 3.161 | |
| formatVCF | 0.793 | 0.094 | 0.940 | |
| getAFTypeIbySumAlleles | 0.544 | 0.069 | 0.652 | |
| getAFs | 0.408 | 0.062 | 0.517 | |
| getBetas | 0.293 | 0.043 | 0.352 | |
| getMask | 2.742 | 0.249 | 3.179 | |
| getRefSet | 5.958 | 0.209 | 6.579 | |
| imputeBetas | 7.708 | 0.725 | 9.054 | |
| imputeBetasByGenomicNeighbors | 14.851 | 0.651 | 16.293 | |
| imputeBetasMatrixByMean | 0 | 0 | 0 | |
| inferEthnicity | 0.001 | 0.000 | 0.000 | |
| inferInfiniumIChannel | 0.145 | 0.229 | 0.394 | |
| inferSex | 9.480 | 0.547 | 10.476 | |
| inferSpecies | 6.805 | 0.352 | 7.454 | |
| inferStrain | 3.624 | 0.237 | 4.095 | |
| inferTissue | 2.407 | 0.369 | 2.930 | |
| initFileSet | 0.364 | 0.069 | 0.465 | |
| listAvailableMasks | 0.397 | 0.069 | 0.484 | |
| mLiftOver | 0.000 | 0.001 | 0.000 | |
| mapFileSet | 0.016 | 0.001 | 0.021 | |
| mapToMammal40 | 0.865 | 0.171 | 1.093 | |
| matchDesign | 4.603 | 0.301 | 5.088 | |
| meanIntensity | 0.985 | 0.110 | 1.154 | |
| medianTotalIntensity | 0.279 | 0.042 | 0.327 | |
| noMasked | 1.332 | 0.094 | 1.492 | |
| noob | 0.846 | 0.095 | 0.966 | |
| openSesame | 1.859 | 0.261 | 2.184 | |
| openSesameToFile | 0.608 | 0.075 | 0.701 | |
| pOOBAH | 0.546 | 0.033 | 0.582 | |
| palgen | 0.017 | 0.003 | 0.020 | |
| parseGEOsignalMU | 1.253 | 0.110 | 1.377 | |
| predictAge | 1.100 | 0.071 | 1.196 | |
| predictAgeHorvath353 | 0 | 0 | 0 | |
| predictAgeSkinBlood | 0 | 0 | 0 | |
| predictMouseAgeInMonth | 0 | 0 | 0 | |
| prefixMask | 0.205 | 0.002 | 0.209 | |
| prefixMaskButC | 0.049 | 0.001 | 0.050 | |
| prefixMaskButCG | 0.018 | 0.001 | 0.018 | |
| prepSesame | 1.266 | 0.132 | 1.446 | |
| prepSesameList | 0.000 | 0.000 | 0.001 | |
| print.DMLSummary | 1.436 | 0.206 | 1.702 | |
| print.fileSet | 0.378 | 0.070 | 0.473 | |
| probeID_designType | 0 | 0 | 0 | |
| probeSuccessRate | 2.217 | 0.210 | 2.546 | |
| qualityMask | 0.543 | 0.076 | 0.659 | |
| reIdentify | 1.858 | 0.079 | 2.021 | |
| readFileSet | 0.036 | 0.004 | 0.040 | |
| readIDATpair | 0.073 | 0.004 | 0.077 | |
| recommendedMaskNames | 0.000 | 0.001 | 0.001 | |
| resetMask | 0.153 | 0.028 | 0.195 | |
| scrub | 0.977 | 0.156 | 1.205 | |
| scrubSoft | 1.484 | 0.404 | 2.031 | |
| sdfPlatform | 0.093 | 0.023 | 0.122 | |
| sdf_read_table | 3.818 | 0.222 | 4.167 | |
| sdf_write_table | 1.148 | 0.067 | 1.238 | |
| searchIDATprefixes | 0.001 | 0.001 | 0.003 | |
| sesame-package | 0.904 | 0.079 | 1.061 | |
| sesameAnno_attachManifest | 0 | 0 | 0 | |
| sesameAnno_buildAddressFile | 0 | 0 | 0 | |
| sesameAnno_buildManifestGRanges | 0 | 0 | 0 | |
| sesameAnno_download | 0 | 0 | 0 | |
| sesameAnno_readManifestTSV | 0 | 0 | 0 | |
| sesameQC_calcStats | 8.417 | 0.850 | 9.816 | |
| sesameQC_getStats | 0.846 | 0.033 | 0.950 | |
| sesameQC_plotBar | 6.899 | 0.217 | 7.569 | |
| sesameQC_plotBetaByDesign | 3.686 | 0.495 | 4.462 | |
| sesameQC_plotHeatSNPs | 8.114 | 0.871 | 9.429 | |
| sesameQC_plotIntensVsBetas | 0.570 | 0.112 | 0.706 | |
| sesameQC_plotRedGrnQQ | 0.573 | 0.116 | 0.725 | |
| sesameQC_rankStats | 1.020 | 0.170 | 1.304 | |
| sesameQCtoDF | 0.939 | 0.072 | 1.083 | |
| sesame_checkVersion | 0.002 | 0.000 | 0.002 | |
| sesamize | 0 | 0 | 0 | |
| setMask | 0.026 | 0.004 | 0.032 | |
| signalMU | 0.272 | 0.037 | 0.327 | |
| sliceFileSet | 0.016 | 0.001 | 0.017 | |
| summaryExtractTest | 1.246 | 0.175 | 1.475 | |
| totalIntensities | 0.931 | 0.107 | 1.085 | |
| updateSigDF | 1.149 | 0.174 | 1.386 | |
| visualizeGene | 3.846 | 0.206 | 4.274 | |
| visualizeProbes | 0.403 | 0.012 | 0.440 | |
| visualizeRegion | 0.114 | 0.012 | 0.132 | |
| visualizeSegments | 0.873 | 0.115 | 1.082 | |