Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-08 12:09 -0400 (Fri, 08 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4815 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
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 1954/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sesame 1.27.1 (landing page) Wanding Zhou
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 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: 1.27.1 |
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_1.27.1.tar.gz |
StartedAt: 2025-08-08 00:04:32 -0400 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 00:17:33 -0400 (Fri, 08 Aug 2025) |
EllapsedTime: 780.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sesame.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.27.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/sesame.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * 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 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 37.692 1.455 39.352 inferSex 23.888 1.318 25.330 sesameQC_calcStats 22.685 1.786 24.626 sesameQC_plotHeatSNPs 19.381 1.942 21.495 imputeBetas 19.272 1.583 20.985 ELBAR 16.661 2.952 19.832 diffRefSet 16.735 0.634 17.493 inferSpecies 15.350 0.675 16.133 sesameQC_plotBar 13.910 0.453 14.484 compareMouseStrainReference 13.495 0.438 14.065 sesameQC_plotBetaByDesign 11.724 1.422 13.278 getRefSet 12.555 0.461 13.102 compareReference 12.141 0.528 12.760 matchDesign 11.335 0.823 12.261 DML 9.036 1.279 10.402 visualizeGene 9.634 0.655 10.379 DMR 9.388 0.301 9.786 sdf_read_table 9.179 0.428 9.670 inferTissue 7.222 1.499 8.816 dyeBiasCorrMostBalanced 8.141 0.338 8.539 inferStrain 7.700 0.608 8.357 estimateLeukocyte 7.425 0.578 8.060 getMask 6.629 0.607 7.298 dyeBiasNL 6.588 0.561 7.208 deIdentify 6.624 0.346 7.015 createUCSCtrack 6.257 0.339 6.648 openSesame 5.679 0.681 6.426 probeSuccessRate 5.617 0.483 6.150 bisConversionControl 4.991 0.258 5.292 reIdentify 4.885 0.291 5.203 * 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/4.5-x86_64/Resources/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)
sesame.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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 22.919 1.931 24.992
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0 | 0 | 0 | |
DML | 9.036 | 1.279 | 10.402 | |
DMLpredict | 1.395 | 0.111 | 1.518 | |
DMR | 9.388 | 0.301 | 9.786 | |
ELBAR | 16.661 | 2.952 | 19.832 | |
MValueToBetaValue | 0 | 0 | 0 | |
SigDF | 0.32 | 0.08 | 0.41 | |
addMask | 0.083 | 0.000 | 0.084 | |
betasCollapseToPfx | 0.011 | 0.000 | 0.012 | |
bisConversionControl | 4.991 | 0.258 | 5.292 | |
calcEffectSize | 1.195 | 0.118 | 1.322 | |
checkLevels | 3.907 | 0.239 | 4.188 | |
cnSegmentation | 0.310 | 0.085 | 0.406 | |
compareMouseStrainReference | 13.495 | 0.438 | 14.065 | |
compareMouseTissueReference | 0.000 | 0.000 | 0.001 | |
compareReference | 12.141 | 0.528 | 12.760 | |
controls | 2.171 | 0.214 | 2.402 | |
createUCSCtrack | 6.257 | 0.339 | 6.648 | |
deIdentify | 6.624 | 0.346 | 7.015 | |
detectionPnegEcdf | 1.409 | 0.014 | 1.430 | |
diffRefSet | 16.735 | 0.634 | 17.493 | |
dmContrasts | 2.069 | 0.217 | 2.297 | |
dyeBiasCorr | 2.988 | 0.250 | 3.255 | |
dyeBiasCorrMostBalanced | 8.141 | 0.338 | 8.539 | |
dyeBiasL | 1.456 | 0.147 | 1.612 | |
dyeBiasNL | 6.588 | 0.561 | 7.208 | |
estimateLeukocyte | 7.425 | 0.578 | 8.060 | |
formatVCF | 2.296 | 0.272 | 2.580 | |
getAFTypeIbySumAlleles | 1.806 | 0.196 | 2.019 | |
getAFs | 1.060 | 0.110 | 1.175 | |
getBetas | 1.848 | 0.126 | 1.985 | |
getMask | 6.629 | 0.607 | 7.298 | |
getRefSet | 12.555 | 0.461 | 13.102 | |
imputeBetas | 19.272 | 1.583 | 20.985 | |
imputeBetasByGenomicNeighbors | 37.692 | 1.455 | 39.352 | |
imputeBetasMatrixByMean | 0.001 | 0.001 | 0.001 | |
inferEthnicity | 0.001 | 0.000 | 0.001 | |
inferInfiniumIChannel | 0.385 | 0.445 | 0.833 | |
inferSex | 23.888 | 1.318 | 25.330 | |
inferSpecies | 15.350 | 0.675 | 16.133 | |
inferStrain | 7.700 | 0.608 | 8.357 | |
inferTissue | 7.222 | 1.499 | 8.816 | |
initFileSet | 1.344 | 0.313 | 1.673 | |
listAvailableMasks | 1.449 | 0.174 | 1.635 | |
mLiftOver | 0.001 | 0.002 | 0.002 | |
mapFileSet | 0.041 | 0.003 | 0.045 | |
mapToMammal40 | 3.236 | 0.390 | 3.662 | |
matchDesign | 11.335 | 0.823 | 12.261 | |
meanIntensity | 2.909 | 0.222 | 3.159 | |
medianTotalIntensity | 0.881 | 0.058 | 0.949 | |
noMasked | 4.136 | 0.225 | 4.394 | |
noob | 2.524 | 0.615 | 3.177 | |
openSesame | 5.679 | 0.681 | 6.426 | |
openSesameToFile | 1.765 | 0.210 | 1.986 | |
pOOBAH | 1.515 | 0.007 | 1.529 | |
palgen | 0.044 | 0.008 | 0.052 | |
parseGEOsignalMU | 3.159 | 0.175 | 3.353 | |
predictAge | 2.672 | 0.123 | 2.817 | |
predictAgeHorvath353 | 0.001 | 0.000 | 0.000 | |
predictAgeSkinBlood | 0 | 0 | 0 | |
predictMouseAgeInMonth | 0 | 0 | 0 | |
prefixMask | 0.631 | 0.002 | 0.637 | |
prefixMaskButC | 0.158 | 0.001 | 0.160 | |
prefixMaskButCG | 0.068 | 0.000 | 0.069 | |
prepSesame | 4.120 | 0.402 | 4.554 | |
prepSesameList | 0.001 | 0.001 | 0.002 | |
print.DMLSummary | 2.940 | 0.747 | 3.733 | |
print.fileSet | 1.236 | 0.258 | 1.504 | |
probeID_designType | 0.001 | 0.000 | 0.001 | |
probeSuccessRate | 5.617 | 0.483 | 6.150 | |
qualityMask | 2.176 | 0.396 | 2.586 | |
reIdentify | 4.885 | 0.291 | 5.203 | |
readFileSet | 0.053 | 0.004 | 0.058 | |
readIDATpair | 0.141 | 0.002 | 0.144 | |
recommendedMaskNames | 0 | 0 | 0 | |
resetMask | 0.402 | 0.072 | 0.476 | |
scrub | 2.410 | 0.018 | 2.439 | |
scrubSoft | 3.365 | 1.154 | 4.564 | |
sdfPlatform | 0.298 | 0.088 | 0.389 | |
sdf_read_table | 9.179 | 0.428 | 9.670 | |
sdf_write_table | 2.732 | 0.161 | 2.927 | |
searchIDATprefixes | 0.003 | 0.003 | 0.006 | |
sesame-package | 2.585 | 0.462 | 3.075 | |
sesameAnno_attachManifest | 0 | 0 | 0 | |
sesameAnno_buildAddressFile | 0.000 | 0.000 | 0.001 | |
sesameAnno_buildManifestGRanges | 0.001 | 0.000 | 0.000 | |
sesameAnno_download | 0.000 | 0.001 | 0.000 | |
sesameAnno_readManifestTSV | 0.000 | 0.000 | 0.001 | |
sesameQC_calcStats | 22.685 | 1.786 | 24.626 | |
sesameQC_getStats | 2.342 | 0.015 | 2.374 | |
sesameQC_plotBar | 13.910 | 0.453 | 14.484 | |
sesameQC_plotBetaByDesign | 11.724 | 1.422 | 13.278 | |
sesameQC_plotHeatSNPs | 19.381 | 1.942 | 21.495 | |
sesameQC_plotIntensVsBetas | 2.278 | 0.458 | 2.778 | |
sesameQC_plotRedGrnQQ | 1.156 | 0.122 | 1.294 | |
sesameQC_rankStats | 3.477 | 0.277 | 3.783 | |
sesameQCtoDF | 2.283 | 0.166 | 2.486 | |
sesame_checkVersion | 0.003 | 0.001 | 0.004 | |
sesamize | 0.000 | 0.001 | 0.001 | |
setMask | 0.122 | 0.001 | 0.123 | |
signalMU | 0.869 | 0.067 | 0.947 | |
sliceFileSet | 0.035 | 0.004 | 0.039 | |
summaryExtractTest | 3.102 | 0.896 | 4.070 | |
totalIntensities | 2.660 | 0.405 | 3.100 | |
updateSigDF | 3.399 | 0.461 | 3.923 | |
visualizeGene | 9.634 | 0.655 | 10.379 | |
visualizeProbes | 1.341 | 0.032 | 1.381 | |
visualizeRegion | 0.367 | 0.010 | 0.377 | |
visualizeSegments | 1.868 | 0.579 | 2.474 | |