Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-29 12:07 -0400 (Mon, 29 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4833 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4621 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4566 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
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 1969/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sesame 1.27.1 (landing page) Wanding Zhou
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
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: 2025-09-26 12:09:20 -0000 (Fri, 26 Sep 2025) |
EndedAt: 2025-09-26 12:25:57 -0000 (Fri, 26 Sep 2025) |
EllapsedTime: 996.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sesame.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 41.464 0.624 53.425 inferSex 26.765 0.313 36.608 imputeBetas 25.507 0.758 32.792 sesameQC_plotHeatSNPs 23.836 0.239 27.044 sesameQC_calcStats 22.628 0.136 25.762 inferSpecies 18.971 0.510 24.274 ELBAR 17.275 0.203 20.124 compareMouseStrainReference 16.823 0.265 22.849 matchDesign 16.301 0.086 21.568 diffRefSet 15.027 0.247 17.991 compareReference 14.024 0.151 18.008 sesameQC_plotBetaByDesign 13.588 0.084 17.221 getRefSet 13.276 0.199 16.348 sesameQC_plotBar 13.168 0.233 14.120 DMR 10.717 0.302 13.844 visualizeGene 9.654 0.279 14.183 DML 9.320 0.343 12.484 inferStrain 9.091 0.262 11.989 sdf_read_table 8.367 0.156 9.987 inferTissue 7.907 0.064 10.915 dyeBiasNL 7.618 0.082 8.731 deIdentify 7.342 0.064 7.867 estimateLeukocyte 7.249 0.150 9.224 getMask 6.850 0.167 8.333 dyeBiasCorrMostBalanced 6.801 0.191 7.402 createUCSCtrack 6.258 0.132 6.748 openSesame 6.052 0.083 7.000 reIdentify 6.039 0.080 6.507 probeSuccessRate 5.677 0.083 6.644 bisConversionControl 4.965 0.072 5.494 sesameQC_rankStats 4.457 0.075 5.807 prepSesame 4.289 0.036 6.418 noMasked 4.119 0.111 5.107 updateSigDF 3.724 0.115 5.716 * 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: ### ### /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)
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 21.467 0.789 26.245
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0.001 | 0.000 | 0.000 | |
DML | 9.320 | 0.343 | 12.484 | |
DMLpredict | 1.462 | 0.040 | 1.518 | |
DMR | 10.717 | 0.302 | 13.844 | |
ELBAR | 17.275 | 0.203 | 20.124 | |
MValueToBetaValue | 0 | 0 | 0 | |
SigDF | 0.350 | 0.024 | 0.751 | |
addMask | 0.091 | 0.004 | 0.192 | |
betasCollapseToPfx | 0.017 | 0.000 | 0.035 | |
bisConversionControl | 4.965 | 0.072 | 5.494 | |
calcEffectSize | 1.353 | 0.028 | 1.537 | |
checkLevels | 3.347 | 0.084 | 4.532 | |
cnSegmentation | 0.338 | 0.032 | 0.374 | |
compareMouseStrainReference | 16.823 | 0.265 | 22.849 | |
compareMouseTissueReference | 0 | 0 | 0 | |
compareReference | 14.024 | 0.151 | 18.008 | |
controls | 2.229 | 0.055 | 2.306 | |
createUCSCtrack | 6.258 | 0.132 | 6.748 | |
deIdentify | 7.342 | 0.064 | 7.867 | |
detectionPnegEcdf | 1.054 | 0.007 | 1.577 | |
diffRefSet | 15.027 | 0.247 | 17.991 | |
dmContrasts | 1.970 | 0.043 | 2.062 | |
dyeBiasCorr | 3.068 | 0.036 | 3.393 | |
dyeBiasCorrMostBalanced | 6.801 | 0.191 | 7.402 | |
dyeBiasL | 2.539 | 0.039 | 2.741 | |
dyeBiasNL | 7.618 | 0.082 | 8.731 | |
estimateLeukocyte | 7.249 | 0.150 | 9.224 | |
formatVCF | 2.300 | 0.040 | 2.857 | |
getAFTypeIbySumAlleles | 1.897 | 0.055 | 2.413 | |
getAFs | 1.339 | 0.020 | 1.450 | |
getBetas | 1.022 | 0.008 | 1.033 | |
getMask | 6.850 | 0.167 | 8.333 | |
getRefSet | 13.276 | 0.199 | 16.348 | |
imputeBetas | 25.507 | 0.758 | 32.792 | |
imputeBetasByGenomicNeighbors | 41.464 | 0.624 | 53.425 | |
imputeBetasMatrixByMean | 0.002 | 0.000 | 0.002 | |
inferEthnicity | 0.001 | 0.000 | 0.001 | |
inferInfiniumIChannel | 0.289 | 0.100 | 0.655 | |
inferSex | 26.765 | 0.313 | 36.608 | |
inferSpecies | 18.971 | 0.510 | 24.274 | |
inferStrain | 9.091 | 0.262 | 11.989 | |
inferTissue | 7.907 | 0.064 | 10.915 | |
initFileSet | 1.343 | 0.032 | 2.271 | |
listAvailableMasks | 1.395 | 0.023 | 1.686 | |
mLiftOver | 0 | 0 | 0 | |
mapFileSet | 0.041 | 0.000 | 0.042 | |
mapToMammal40 | 2.734 | 0.040 | 3.175 | |
matchDesign | 16.301 | 0.086 | 21.568 | |
meanIntensity | 3.000 | 0.115 | 3.392 | |
medianTotalIntensity | 1.000 | 0.036 | 1.043 | |
noMasked | 4.119 | 0.111 | 5.107 | |
noob | 2.496 | 0.011 | 2.705 | |
openSesame | 6.052 | 0.083 | 7.000 | |
openSesameToFile | 1.843 | 0.016 | 1.996 | |
pOOBAH | 1.428 | 0.000 | 1.518 | |
palgen | 0.042 | 0.004 | 0.061 | |
parseGEOsignalMU | 3.167 | 0.084 | 4.603 | |
predictAge | 2.620 | 0.039 | 3.190 | |
predictAgeHorvath353 | 0 | 0 | 0 | |
predictAgeSkinBlood | 0 | 0 | 0 | |
predictMouseAgeInMonth | 0.000 | 0.000 | 0.001 | |
prefixMask | 0.539 | 0.000 | 0.545 | |
prefixMaskButC | 0.159 | 0.000 | 0.206 | |
prefixMaskButCG | 0.068 | 0.000 | 0.137 | |
prepSesame | 4.289 | 0.036 | 6.418 | |
prepSesameList | 0.001 | 0.000 | 0.001 | |
print.DMLSummary | 3.002 | 0.143 | 3.430 | |
print.fileSet | 1.312 | 0.032 | 1.632 | |
probeID_designType | 0 | 0 | 0 | |
probeSuccessRate | 5.677 | 0.083 | 6.644 | |
qualityMask | 1.979 | 0.059 | 2.662 | |
reIdentify | 6.039 | 0.080 | 6.507 | |
readFileSet | 0.051 | 0.004 | 0.057 | |
readIDATpair | 0.137 | 0.003 | 0.139 | |
recommendedMaskNames | 0 | 0 | 0 | |
resetMask | 0.467 | 0.028 | 0.496 | |
scrub | 2.900 | 0.067 | 3.245 | |
scrubSoft | 4.435 | 0.064 | 4.946 | |
sdfPlatform | 0.327 | 0.039 | 0.368 | |
sdf_read_table | 8.367 | 0.156 | 9.987 | |
sdf_write_table | 2.352 | 0.059 | 3.228 | |
searchIDATprefixes | 0.005 | 0.000 | 0.020 | |
sesame-package | 2.605 | 0.056 | 2.742 | |
sesameAnno_attachManifest | 0 | 0 | 0 | |
sesameAnno_buildAddressFile | 0 | 0 | 0 | |
sesameAnno_buildManifestGRanges | 0 | 0 | 0 | |
sesameAnno_download | 0.000 | 0.000 | 0.001 | |
sesameAnno_readManifestTSV | 0 | 0 | 0 | |
sesameQC_calcStats | 22.628 | 0.136 | 25.762 | |
sesameQC_getStats | 2.251 | 0.004 | 2.270 | |
sesameQC_plotBar | 13.168 | 0.233 | 14.120 | |
sesameQC_plotBetaByDesign | 13.588 | 0.084 | 17.221 | |
sesameQC_plotHeatSNPs | 23.836 | 0.239 | 27.044 | |
sesameQC_plotIntensVsBetas | 2.447 | 0.036 | 2.967 | |
sesameQC_plotRedGrnQQ | 1.572 | 0.028 | 3.207 | |
sesameQC_rankStats | 4.457 | 0.075 | 5.807 | |
sesameQCtoDF | 1.987 | 0.003 | 2.054 | |
sesame_checkVersion | 0.004 | 0.000 | 0.004 | |
sesamize | 0.001 | 0.000 | 0.007 | |
setMask | 0.121 | 0.000 | 0.141 | |
signalMU | 1.238 | 0.008 | 1.271 | |
sliceFileSet | 0.040 | 0.001 | 0.041 | |
summaryExtractTest | 3.025 | 0.047 | 3.244 | |
totalIntensities | 2.932 | 0.080 | 3.866 | |
updateSigDF | 3.724 | 0.115 | 5.716 | |
visualizeGene | 9.654 | 0.279 | 14.183 | |
visualizeProbes | 1.596 | 0.012 | 1.926 | |
visualizeRegion | 0.453 | 0.000 | 0.548 | |
visualizeSegments | 1.772 | 0.119 | 1.985 | |