Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-19 12:12 -0400 (Wed, 19 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4687 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4402 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4351 |
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 1900/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sesame 1.23.6 (landing page) Wanding Zhou
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 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: 1.23.6 |
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_1.23.6.tar.gz |
StartedAt: 2024-06-18 23:59:05 -0400 (Tue, 18 Jun 2024) |
EndedAt: 2024-06-19 00:04:33 -0400 (Wed, 19 Jun 2024) |
EllapsedTime: 328.7 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_1.23.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.23.6’ * 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 testEnrichmentGene 16.105 0.908 18.628 imputeBetasByGenomicNeighbors 12.599 0.458 13.331 inferSex 8.290 0.387 8.867 sesameQC_calcStats 7.518 0.520 8.126 KYCG_plotMeta 7.499 0.291 7.961 sesameQC_plotHeatSNPs 6.961 0.598 7.695 KYCG_plotEnrichAll 6.696 0.237 7.334 imputeBetas 6.310 0.438 7.057 sesameQC_plotBar 6.061 0.168 6.503 inferSpecies 5.595 0.229 6.117 ELBAR 4.883 0.770 5.707 diffRefSet 5.101 0.274 5.556 matchDesign 4.822 0.204 5.115 KYCG_annoProbes 4.785 0.234 5.241 KYCG_buildGeneDBs 4.743 0.153 5.020 * 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/4.4-arm64/Resources/library’ * installing *source* package ‘sesame’ ... ** 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 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" Copyright (C) 2024 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 Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, tapply, union, 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 7.438 0.406 8.198
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0 | 0 | 0 | |
DML | 2.328 | 0.259 | 2.813 | |
DMLpredict | 0.349 | 0.028 | 0.433 | |
DMR | 2.719 | 0.077 | 3.018 | |
ELBAR | 4.883 | 0.770 | 5.707 | |
KYCG_annoProbes | 4.785 | 0.234 | 5.241 | |
KYCG_buildGeneDBs | 4.743 | 0.153 | 5.020 | |
KYCG_getDBs | 0.846 | 0.075 | 1.031 | |
KYCG_listDBGroups | 0.009 | 0.001 | 0.011 | |
KYCG_loadDBs | 0 | 0 | 0 | |
KYCG_plotBar | 0.064 | 0.006 | 0.071 | |
KYCG_plotDot | 0.205 | 0.007 | 0.212 | |
KYCG_plotEnrichAll | 6.696 | 0.237 | 7.334 | |
KYCG_plotLollipop | 0.046 | 0.004 | 0.051 | |
KYCG_plotManhattan | 0.567 | 0.023 | 0.590 | |
KYCG_plotMeta | 7.499 | 0.291 | 7.961 | |
KYCG_plotMetaEnrichment | 3.808 | 0.182 | 4.175 | |
KYCG_plotPointRange | 0.678 | 0.072 | 0.806 | |
KYCG_plotSetEnrichment | 1.843 | 0.132 | 2.094 | |
KYCG_plotVolcano | 0.042 | 0.000 | 0.043 | |
KYCG_plotWaterfall | 1.238 | 0.068 | 1.363 | |
MValueToBetaValue | 0 | 0 | 0 | |
SigDF | 0.086 | 0.012 | 0.154 | |
addMask | 0.016 | 0.001 | 0.017 | |
aggregateTestEnrichments | 0.385 | 0.023 | 0.409 | |
betasCollapseToPfx | 0.004 | 0.000 | 0.004 | |
bisConversionControl | 2.290 | 0.059 | 2.476 | |
calcEffectSize | 0.350 | 0.026 | 0.466 | |
checkLevels | 1.072 | 0.109 | 1.277 | |
cnSegmentation | 0.088 | 0.017 | 0.195 | |
compareMouseStrainReference | 3.366 | 0.128 | 3.674 | |
compareMouseTissueReference | 0 | 0 | 0 | |
compareReference | 3.871 | 0.151 | 4.228 | |
controls | 0.688 | 0.062 | 0.934 | |
createUCSCtrack | 2.061 | 0.137 | 2.389 | |
dbStats | 1.961 | 0.168 | 2.310 | |
deidentify | 1.642 | 0.104 | 1.949 | |
detectionPnegEcdf | 0.956 | 0.045 | 1.090 | |
diffRefSet | 5.101 | 0.274 | 5.556 | |
dmContrasts | 0.618 | 0.030 | 0.745 | |
dyeBiasCorr | 0.808 | 0.099 | 1.091 | |
dyeBiasCorrMostBalanced | 2.860 | 0.073 | 3.118 | |
dyeBiasL | 0.849 | 0.050 | 1.055 | |
dyeBiasNL | 2.172 | 0.136 | 2.465 | |
estimateLeukocyte | 2.213 | 0.103 | 2.501 | |
formatVCF | 0.706 | 0.041 | 0.926 | |
getAFTypeIbySumAlleles | 0.547 | 0.094 | 0.822 | |
getAFs | 0.370 | 0.036 | 0.496 | |
getBetas | 0.271 | 0.029 | 0.388 | |
getMask | 2.065 | 0.159 | 2.591 | |
getRefSet | 4.502 | 0.095 | 4.785 | |
imputeBetas | 6.310 | 0.438 | 7.057 | |
imputeBetasByGenomicNeighbors | 12.599 | 0.458 | 13.331 | |
imputeBetasMatrixByMean | 0.000 | 0.000 | 0.001 | |
inferEthnicity | 0 | 0 | 0 | |
inferInfiniumIChannel | 0.130 | 0.139 | 0.273 | |
inferSex | 8.290 | 0.387 | 8.867 | |
inferSpecies | 5.595 | 0.229 | 6.117 | |
inferStrain | 2.705 | 0.258 | 3.143 | |
inferTissue | 2.354 | 0.249 | 2.785 | |
initFileSet | 0.345 | 0.041 | 0.475 | |
listAvailableMasks | 0.365 | 0.036 | 0.491 | |
mLiftOver | 0 | 0 | 0 | |
mapFileSet | 0.015 | 0.002 | 0.016 | |
mapToMammal40 | 0.822 | 0.143 | 1.211 | |
matchDesign | 4.822 | 0.204 | 5.115 | |
meanIntensity | 0.915 | 0.102 | 1.199 | |
medianTotalIntensity | 0.239 | 0.039 | 0.368 | |
noMasked | 1.076 | 0.107 | 1.361 | |
noob | 0.802 | 0.116 | 0.918 | |
openSesame | 1.571 | 0.178 | 1.931 | |
openSesameToFile | 0.514 | 0.044 | 0.558 | |
pOOBAH | 0.486 | 0.022 | 0.509 | |
palgen | 0.016 | 0.003 | 0.020 | |
parseGEOsignalMU | 1.182 | 0.104 | 1.379 | |
predictAge | 0.845 | 0.034 | 0.969 | |
predictAgeHorvath353 | 0 | 0 | 0 | |
predictAgeSkinBlood | 0 | 0 | 0 | |
predictMouseAgeInMonth | 0 | 0 | 0 | |
prefixMask | 0.266 | 0.002 | 0.268 | |
prefixMaskButC | 0.077 | 0.000 | 0.077 | |
prefixMaskButCG | 0.034 | 0.000 | 0.034 | |
prepSesame | 1.259 | 0.100 | 1.447 | |
prepSesameList | 0 | 0 | 0 | |
print.DMLSummary | 1.039 | 0.155 | 1.403 | |
print.fileSet | 0.326 | 0.031 | 0.469 | |
probeID_designType | 0 | 0 | 0 | |
probeSuccessRate | 1.928 | 0.221 | 2.426 | |
qualityMask | 0.655 | 0.079 | 0.933 | |
reIdentify | 1.417 | 0.069 | 1.592 | |
readFileSet | 0.027 | 0.001 | 0.028 | |
readIDATpair | 0.048 | 0.004 | 0.053 | |
recommendedMaskNames | 0.000 | 0.000 | 0.001 | |
resetMask | 0.109 | 0.018 | 0.216 | |
scrub | 0.905 | 0.098 | 1.002 | |
scrubSoft | 1.264 | 0.230 | 1.494 | |
sdfPlatform | 0.075 | 0.010 | 0.174 | |
sdf_read_table | 3.142 | 0.155 | 3.478 | |
sdf_write_table | 0.905 | 0.035 | 1.031 | |
searchIDATprefixes | 0.001 | 0.001 | 0.003 | |
sesame-package | 0.837 | 0.108 | 1.037 | |
sesameAnno_buildAddressFile | 0 | 0 | 0 | |
sesameAnno_buildManifestGRanges | 0 | 0 | 0 | |
sesameAnno_download | 0 | 0 | 0 | |
sesameAnno_get | 0 | 0 | 0 | |
sesameAnno_readManifestTSV | 0 | 0 | 0 | |
sesameData_getAnno | 0 | 0 | 0 | |
sesameQC_calcStats | 7.518 | 0.520 | 8.126 | |
sesameQC_getStats | 0.746 | 0.026 | 0.772 | |
sesameQC_plotBar | 6.061 | 0.168 | 6.503 | |
sesameQC_plotBetaByDesign | 4.256 | 0.502 | 4.761 | |
sesameQC_plotHeatSNPs | 6.961 | 0.598 | 7.695 | |
sesameQC_plotIntensVsBetas | 0.599 | 0.115 | 0.864 | |
sesameQC_plotRedGrnQQ | 0.458 | 0.049 | 0.639 | |
sesameQC_rankStats | 1.136 | 0.152 | 1.550 | |
sesameQCtoDF | 0.844 | 0.032 | 0.875 | |
sesame_checkVersion | 0.002 | 0.001 | 0.001 | |
sesamize | 0 | 0 | 0 | |
setMask | 0.025 | 0.005 | 0.029 | |
signalMU | 0.242 | 0.031 | 0.506 | |
sliceFileSet | 0.013 | 0.001 | 0.014 | |
summaryExtractTest | 1.104 | 0.122 | 1.580 | |
testEnrichment | 1.755 | 0.163 | 2.329 | |
testEnrichmentGene | 16.105 | 0.908 | 18.628 | |
testEnrichmentSEA | 3.687 | 0.273 | 4.352 | |
totalIntensities | 1.078 | 0.063 | 1.402 | |
updateSigDF | 1.819 | 0.111 | 2.200 | |
visualizeGene | 3.564 | 0.154 | 4.113 | |
visualizeProbes | 0.448 | 0.010 | 0.458 | |
visualizeRegion | 0.096 | 0.003 | 0.100 | |
visualizeSegments | 0.865 | 0.089 | 1.090 | |