Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-16 11:44 -0400 (Tue, 16 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" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 1901/2243 | 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 | ![]() | ||||||||
palomino6 | 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 | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | 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: 2024-07-16 00:04:51 -0400 (Tue, 16 Jul 2024) |
EndedAt: 2024-07-16 00:10:16 -0400 (Tue, 16 Jul 2024) |
EllapsedTime: 324.6 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 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.23.8’ * 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 16.271 1.019 18.025 imputeBetasByGenomicNeighbors 12.724 0.451 13.355 inferSex 8.296 0.388 8.839 sesameQC_calcStats 7.851 0.546 8.461 sesameQC_plotHeatSNPs 7.485 0.535 8.081 KYCG_plotMeta 6.837 0.314 7.334 imputeBetas 6.449 0.492 7.115 KYCG_plotEnrichAll 6.581 0.263 7.269 sesameQC_plotBar 6.049 0.123 6.283 inferSpecies 5.745 0.277 6.210 ELBAR 5.125 0.746 5.933 KYCG_annoProbes 5.126 0.196 5.548 diffRefSet 5.054 0.240 5.412 testEnrichmentSEA 4.506 0.407 5.093 * 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 7.561 0.429 8.111
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0 | 0 | 0 | |
DML | 2.432 | 0.272 | 2.874 | |
DMLpredict | 0.398 | 0.033 | 0.486 | |
DMR | 2.847 | 0.072 | 3.035 | |
ELBAR | 5.125 | 0.746 | 5.933 | |
KYCG_annoProbes | 5.126 | 0.196 | 5.548 | |
KYCG_buildGeneDBs | 4.520 | 0.136 | 4.773 | |
KYCG_getDBs | 0.823 | 0.099 | 1.034 | |
KYCG_listDBGroups | 0.010 | 0.001 | 0.011 | |
KYCG_loadDBs | 0 | 0 | 0 | |
KYCG_plotBar | 0.058 | 0.008 | 0.066 | |
KYCG_plotDot | 0.187 | 0.012 | 0.199 | |
KYCG_plotEnrichAll | 6.581 | 0.263 | 7.269 | |
KYCG_plotLollipop | 0.046 | 0.003 | 0.049 | |
KYCG_plotManhattan | 0.542 | 0.020 | 0.562 | |
KYCG_plotMeta | 6.837 | 0.314 | 7.334 | |
KYCG_plotMetaEnrichment | 4.070 | 0.204 | 4.450 | |
KYCG_plotPointRange | 0.657 | 0.064 | 0.779 | |
KYCG_plotSetEnrichment | 1.859 | 0.169 | 2.142 | |
KYCG_plotVolcano | 0.044 | 0.004 | 0.047 | |
KYCG_plotWaterfall | 0.777 | 0.057 | 0.895 | |
MValueToBetaValue | 0 | 0 | 0 | |
SigDF | 0.084 | 0.014 | 0.155 | |
addMask | 0.017 | 0.002 | 0.019 | |
aggregateTestEnrichments | 0.555 | 0.034 | 0.589 | |
betasCollapseToPfx | 0.006 | 0.000 | 0.005 | |
bisConversionControl | 2.230 | 0.056 | 2.413 | |
calcEffectSize | 0.485 | 0.084 | 0.629 | |
checkLevels | 1.091 | 0.103 | 1.254 | |
cnSegmentation | 0.089 | 0.014 | 0.159 | |
compareMouseStrainReference | 3.498 | 0.133 | 3.745 | |
compareMouseTissueReference | 0 | 0 | 0 | |
compareReference | 3.757 | 0.155 | 4.027 | |
controls | 0.698 | 0.080 | 0.898 | |
createUCSCtrack | 2.110 | 0.142 | 2.369 | |
dbStats | 2.239 | 0.186 | 2.538 | |
deidentify | 1.738 | 0.104 | 1.958 | |
detectionPnegEcdf | 0.906 | 0.052 | 1.014 | |
diffRefSet | 5.054 | 0.240 | 5.412 | |
dmContrasts | 0.677 | 0.074 | 0.811 | |
dyeBiasCorr | 0.933 | 0.073 | 1.161 | |
dyeBiasCorrMostBalanced | 2.844 | 0.063 | 3.021 | |
dyeBiasL | 0.893 | 0.059 | 1.009 | |
dyeBiasNL | 1.885 | 0.135 | 2.076 | |
estimateLeukocyte | 2.654 | 0.141 | 2.924 | |
formatVCF | 0.653 | 0.061 | 0.827 | |
getAFTypeIbySumAlleles | 0.524 | 0.079 | 0.716 | |
getAFs | 0.322 | 0.032 | 0.408 | |
getBetas | 0.231 | 0.024 | 0.310 | |
getMask | 2.043 | 0.154 | 2.420 | |
getRefSet | 4.277 | 0.242 | 4.634 | |
imputeBetas | 6.449 | 0.492 | 7.115 | |
imputeBetasByGenomicNeighbors | 12.724 | 0.451 | 13.355 | |
imputeBetasMatrixByMean | 0.000 | 0.000 | 0.001 | |
inferEthnicity | 0.001 | 0.000 | 0.000 | |
inferInfiniumIChannel | 0.144 | 0.150 | 0.302 | |
inferSex | 8.296 | 0.388 | 8.839 | |
inferSpecies | 5.745 | 0.277 | 6.210 | |
inferStrain | 2.819 | 0.201 | 3.137 | |
inferTissue | 2.397 | 0.297 | 2.808 | |
initFileSet | 0.353 | 0.075 | 0.484 | |
listAvailableMasks | 0.382 | 0.083 | 0.520 | |
mLiftOver | 0.001 | 0.000 | 0.001 | |
mapFileSet | 0.015 | 0.003 | 0.019 | |
mapToMammal40 | 0.702 | 0.092 | 0.908 | |
matchDesign | 4.409 | 0.221 | 4.688 | |
meanIntensity | 0.926 | 0.096 | 1.133 | |
medianTotalIntensity | 0.264 | 0.028 | 0.348 | |
noMasked | 1.226 | 0.073 | 1.418 | |
noob | 0.804 | 0.111 | 0.915 | |
openSesame | 1.584 | 0.180 | 1.885 | |
openSesameToFile | 0.479 | 0.031 | 0.510 | |
pOOBAH | 0.462 | 0.026 | 0.488 | |
palgen | 0.015 | 0.003 | 0.018 | |
parseGEOsignalMU | 1.173 | 0.094 | 1.324 | |
predictAge | 0.924 | 0.055 | 1.035 | |
predictAgeHorvath353 | 0.001 | 0.000 | 0.000 | |
predictAgeSkinBlood | 0 | 0 | 0 | |
predictMouseAgeInMonth | 0 | 0 | 0 | |
prefixMask | 0.281 | 0.002 | 0.283 | |
prefixMaskButC | 0.080 | 0.001 | 0.081 | |
prefixMaskButCG | 0.033 | 0.000 | 0.033 | |
prepSesame | 1.311 | 0.103 | 1.471 | |
prepSesameList | 0.000 | 0.001 | 0.001 | |
print.DMLSummary | 1.169 | 0.149 | 1.443 | |
print.fileSet | 0.368 | 0.075 | 0.504 | |
probeID_designType | 0.000 | 0.000 | 0.001 | |
probeSuccessRate | 1.954 | 0.216 | 2.341 | |
qualityMask | 0.645 | 0.078 | 0.835 | |
reIdentify | 1.420 | 0.057 | 1.538 | |
readFileSet | 0.026 | 0.001 | 0.027 | |
readIDATpair | 0.040 | 0.004 | 0.045 | |
recommendedMaskNames | 0.000 | 0.000 | 0.001 | |
resetMask | 0.113 | 0.025 | 0.234 | |
scrub | 0.859 | 0.114 | 0.974 | |
scrubSoft | 1.265 | 0.240 | 1.505 | |
sdfPlatform | 0.084 | 0.016 | 0.157 | |
sdf_read_table | 3.215 | 0.147 | 3.485 | |
sdf_write_table | 0.920 | 0.041 | 1.025 | |
searchIDATprefixes | 0.001 | 0.000 | 0.004 | |
sesame-package | 0.880 | 0.112 | 1.049 | |
sesameAnno_attachManifest | 0 | 0 | 0 | |
sesameAnno_buildAddressFile | 0 | 0 | 0 | |
sesameAnno_buildManifestGRanges | 0 | 0 | 0 | |
sesameAnno_download | 0 | 0 | 0 | |
sesameAnno_readManifestTSV | 0.000 | 0.001 | 0.000 | |
sesameQC_calcStats | 7.851 | 0.546 | 8.461 | |
sesameQC_getStats | 0.762 | 0.037 | 0.799 | |
sesameQC_plotBar | 6.049 | 0.123 | 6.283 | |
sesameQC_plotBetaByDesign | 3.919 | 0.475 | 4.396 | |
sesameQC_plotHeatSNPs | 7.485 | 0.535 | 8.081 | |
sesameQC_plotIntensVsBetas | 0.617 | 0.123 | 0.838 | |
sesameQC_plotRedGrnQQ | 0.441 | 0.055 | 0.557 | |
sesameQC_rankStats | 1.024 | 0.164 | 1.298 | |
sesameQCtoDF | 0.847 | 0.046 | 0.892 | |
sesame_checkVersion | 0.001 | 0.000 | 0.001 | |
sesamize | 0 | 0 | 0 | |
setMask | 0.021 | 0.002 | 0.023 | |
signalMU | 0.241 | 0.034 | 0.330 | |
sliceFileSet | 0.016 | 0.001 | 0.016 | |
summaryExtractTest | 0.993 | 0.105 | 1.222 | |
testEnrichment | 1.817 | 0.260 | 2.254 | |
testEnrichmentGene | 16.271 | 1.019 | 18.025 | |
testEnrichmentSEA | 4.506 | 0.407 | 5.093 | |
totalIntensities | 1.197 | 0.104 | 1.432 | |
updateSigDF | 0.889 | 0.070 | 1.072 | |
visualizeGene | 3.704 | 0.148 | 4.026 | |
visualizeProbes | 0.262 | 0.005 | 0.268 | |
visualizeRegion | 0.202 | 0.007 | 0.210 | |
visualizeSegments | 1.089 | 0.117 | 1.266 | |