Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-24 11:42 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4284 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
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 1906/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sesame 1.23.8 (landing page) Wanding Zhou
| nebbiolo2 | Linux (Ubuntu 22.04.3 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 13.6.5 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: 1.23.8 |
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_1.23.8.tar.gz |
StartedAt: 2024-07-24 00:53:38 -0400 (Wed, 24 Jul 2024) |
EndedAt: 2024-07-24 00:59:13 -0400 (Wed, 24 Jul 2024) |
EllapsedTime: 335.7 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_1.23.8.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.23.8’ * 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 16.912 1.095 18.736 imputeBetasByGenomicNeighbors 13.524 0.507 14.220 inferSex 9.397 0.455 10.048 sesameQC_calcStats 8.413 0.626 9.109 KYCG_plotMeta 7.520 0.331 8.023 sesameQC_plotHeatSNPs 7.261 0.588 7.958 imputeBetas 7.264 0.546 7.988 KYCG_plotEnrichAll 6.564 0.282 7.259 sesameQC_plotBar 6.145 0.149 6.418 ELBAR 5.097 0.815 5.982 inferSpecies 5.336 0.314 5.834 KYCG_annoProbes 5.209 0.223 5.612 diffRefSet 5.229 0.186 5.539 getRefSet 5.050 0.203 5.388 * 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 (2024-06-14) -- "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': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, 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 7.550 0.407 8.183
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0 | 0 | 0 | |
DML | 2.514 | 0.266 | 2.948 | |
DMLpredict | 0.410 | 0.034 | 0.568 | |
DMR | 2.894 | 0.076 | 3.113 | |
ELBAR | 5.097 | 0.815 | 5.982 | |
KYCG_annoProbes | 5.209 | 0.223 | 5.612 | |
KYCG_buildGeneDBs | 4.602 | 0.167 | 4.887 | |
KYCG_getDBs | 0.885 | 0.059 | 1.060 | |
KYCG_listDBGroups | 0.010 | 0.000 | 0.011 | |
KYCG_loadDBs | 0.000 | 0.000 | 0.001 | |
KYCG_plotBar | 0.059 | 0.005 | 0.065 | |
KYCG_plotDot | 0.186 | 0.007 | 0.193 | |
KYCG_plotEnrichAll | 6.564 | 0.282 | 7.259 | |
KYCG_plotLollipop | 0.047 | 0.003 | 0.051 | |
KYCG_plotManhattan | 0.608 | 0.059 | 0.667 | |
KYCG_plotMeta | 7.520 | 0.331 | 8.023 | |
KYCG_plotMetaEnrichment | 4.208 | 0.198 | 4.591 | |
KYCG_plotPointRange | 0.736 | 0.071 | 0.864 | |
KYCG_plotSetEnrichment | 1.826 | 0.175 | 2.115 | |
KYCG_plotVolcano | 0.043 | 0.001 | 0.043 | |
KYCG_plotWaterfall | 0.825 | 0.072 | 0.957 | |
MValueToBetaValue | 0 | 0 | 0 | |
SigDF | 0.083 | 0.014 | 0.152 | |
addMask | 0.015 | 0.002 | 0.017 | |
aggregateTestEnrichments | 0.541 | 0.049 | 0.590 | |
betasCollapseToPfx | 0.004 | 0.000 | 0.005 | |
bisConversionControl | 2.223 | 0.083 | 2.416 | |
calcEffectSize | 0.471 | 0.038 | 0.563 | |
checkLevels | 1.102 | 0.064 | 1.222 | |
cnSegmentation | 0.083 | 0.011 | 0.150 | |
compareMouseStrainReference | 3.672 | 0.190 | 3.974 | |
compareMouseTissueReference | 0 | 0 | 0 | |
compareReference | 3.719 | 0.123 | 3.955 | |
controls | 0.662 | 0.045 | 0.828 | |
createUCSCtrack | 2.191 | 0.144 | 2.450 | |
dbStats | 2.333 | 0.257 | 2.720 | |
deidentify | 1.738 | 0.134 | 2.033 | |
detectionPnegEcdf | 1.004 | 0.088 | 1.156 | |
diffRefSet | 5.229 | 0.186 | 5.539 | |
dmContrasts | 0.709 | 0.103 | 0.873 | |
dyeBiasCorr | 0.930 | 0.116 | 1.157 | |
dyeBiasCorrMostBalanced | 2.947 | 0.120 | 3.202 | |
dyeBiasL | 0.920 | 0.060 | 1.038 | |
dyeBiasNL | 1.560 | 0.110 | 1.726 | |
estimateLeukocyte | 2.638 | 0.124 | 2.880 | |
formatVCF | 0.715 | 0.089 | 0.919 | |
getAFTypeIbySumAlleles | 0.538 | 0.083 | 0.740 | |
getAFs | 0.371 | 0.043 | 0.472 | |
getBetas | 0.256 | 0.029 | 0.340 | |
getMask | 2.230 | 0.247 | 2.727 | |
getRefSet | 5.050 | 0.203 | 5.388 | |
imputeBetas | 7.264 | 0.546 | 7.988 | |
imputeBetasByGenomicNeighbors | 13.524 | 0.507 | 14.220 | |
imputeBetasMatrixByMean | 0.000 | 0.000 | 0.001 | |
inferEthnicity | 0.001 | 0.000 | 0.000 | |
inferInfiniumIChannel | 0.132 | 0.142 | 0.277 | |
inferSex | 9.397 | 0.455 | 10.048 | |
inferSpecies | 5.336 | 0.314 | 5.834 | |
inferStrain | 2.723 | 0.265 | 3.111 | |
inferTissue | 2.146 | 0.293 | 2.550 | |
initFileSet | 0.377 | 0.040 | 0.471 | |
listAvailableMasks | 0.415 | 0.037 | 0.508 | |
mLiftOver | 0 | 0 | 0 | |
mapFileSet | 0.016 | 0.001 | 0.017 | |
mapToMammal40 | 0.834 | 0.139 | 1.089 | |
matchDesign | 4.262 | 0.212 | 4.533 | |
meanIntensity | 0.907 | 0.092 | 1.154 | |
medianTotalIntensity | 0.258 | 0.033 | 0.347 | |
noMasked | 1.175 | 0.085 | 1.378 | |
noob | 0.860 | 0.109 | 0.968 | |
openSesame | 1.639 | 0.175 | 1.938 | |
openSesameToFile | 0.541 | 0.043 | 0.583 | |
pOOBAH | 0.513 | 0.022 | 0.537 | |
palgen | 0.017 | 0.004 | 0.022 | |
parseGEOsignalMU | 1.256 | 0.107 | 1.423 | |
predictAge | 0.94 | 0.04 | 1.04 | |
predictAgeHorvath353 | 0 | 0 | 0 | |
predictAgeSkinBlood | 0 | 0 | 0 | |
predictMouseAgeInMonth | 0 | 0 | 0 | |
prefixMask | 0.196 | 0.002 | 0.198 | |
prefixMaskButC | 0.051 | 0.001 | 0.053 | |
prefixMaskButCG | 0.018 | 0.001 | 0.019 | |
prepSesame | 1.375 | 0.115 | 1.546 | |
prepSesameList | 0 | 0 | 0 | |
print.DMLSummary | 1.103 | 0.145 | 1.360 | |
print.fileSet | 0.360 | 0.039 | 0.452 | |
probeID_designType | 0.000 | 0.000 | 0.001 | |
probeSuccessRate | 1.967 | 0.139 | 2.279 | |
qualityMask | 0.710 | 0.077 | 0.921 | |
reIdentify | 1.437 | 0.037 | 1.528 | |
readFileSet | 0.026 | 0.001 | 0.027 | |
readIDATpair | 0.040 | 0.003 | 0.044 | |
recommendedMaskNames | 0.000 | 0.000 | 0.001 | |
resetMask | 0.106 | 0.022 | 0.184 | |
scrub | 0.922 | 0.104 | 1.026 | |
scrubSoft | 1.380 | 0.266 | 1.649 | |
sdfPlatform | 0.087 | 0.012 | 0.156 | |
sdf_read_table | 3.315 | 0.148 | 3.595 | |
sdf_write_table | 0.927 | 0.035 | 1.019 | |
searchIDATprefixes | 0.002 | 0.001 | 0.003 | |
sesame-package | 0.911 | 0.086 | 1.063 | |
sesameAnno_attachManifest | 0.000 | 0.001 | 0.000 | |
sesameAnno_buildAddressFile | 0 | 0 | 0 | |
sesameAnno_buildManifestGRanges | 0.000 | 0.000 | 0.001 | |
sesameAnno_download | 0 | 0 | 0 | |
sesameAnno_readManifestTSV | 0 | 0 | 0 | |
sesameQC_calcStats | 8.413 | 0.626 | 9.109 | |
sesameQC_getStats | 0.858 | 0.055 | 0.913 | |
sesameQC_plotBar | 6.145 | 0.149 | 6.418 | |
sesameQC_plotBetaByDesign | 3.594 | 0.491 | 4.102 | |
sesameQC_plotHeatSNPs | 7.261 | 0.588 | 7.958 | |
sesameQC_plotIntensVsBetas | 0.647 | 0.102 | 0.816 | |
sesameQC_plotRedGrnQQ | 0.450 | 0.061 | 0.570 | |
sesameQC_rankStats | 1.161 | 0.165 | 1.439 | |
sesameQCtoDF | 0.769 | 0.028 | 0.797 | |
sesame_checkVersion | 0.002 | 0.001 | 0.001 | |
sesamize | 0.000 | 0.000 | 0.001 | |
setMask | 0.023 | 0.003 | 0.026 | |
signalMU | 0.338 | 0.062 | 0.498 | |
sliceFileSet | 0.014 | 0.001 | 0.016 | |
summaryExtractTest | 1.108 | 0.136 | 1.355 | |
testEnrichment | 1.848 | 0.209 | 2.292 | |
testEnrichmentGene | 16.912 | 1.095 | 18.736 | |
testEnrichmentSEA | 3.966 | 0.319 | 4.464 | |
totalIntensities | 1.148 | 0.089 | 1.352 | |
updateSigDF | 1.039 | 0.133 | 1.288 | |
visualizeGene | 3.752 | 0.147 | 4.068 | |
visualizeProbes | 0.272 | 0.007 | 0.279 | |
visualizeRegion | 1.021 | 0.040 | 1.061 | |
visualizeSegments | 0.881 | 0.087 | 1.024 | |