Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-27 11:38:07 -0400 (Wed, 27 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4667 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4403 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4426 |
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 1934/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sesame 1.20.0 (landing page) Wanding Zhou
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.20.0 |
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_1.20.0.tar.gz |
StartedAt: 2024-03-26 08:36:45 -0400 (Tue, 26 Mar 2024) |
EndedAt: 2024-03-26 09:05:58 -0400 (Tue, 26 Mar 2024) |
EllapsedTime: 1753.5 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_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/sesame.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.20.0’ * 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 R 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 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 175.584 7.063 202.861 sesameQC_calcStats 36.198 1.715 38.584 KYCG_plotMeta 31.679 1.148 34.791 sesameQC_plotHeatSNPs 29.858 1.789 32.851 KYCG_plotEnrichAll 29.298 1.327 33.564 compareMouseStrainReference 29.187 0.574 32.156 compareReference 26.708 0.864 30.145 inferSpecies 24.557 1.002 28.703 ELBAR 21.638 2.889 26.531 matchDesign 23.327 0.768 25.604 diffRefSet 21.465 0.861 24.327 KYCG_annoProbes 21.354 0.962 23.640 convertTo 20.615 0.607 23.651 sesameQC_plotBar 19.484 0.681 21.317 getRefSet 19.236 0.683 21.924 testEnrichmentSEA 18.278 0.959 21.112 DML 16.186 1.904 20.271 inferTissue 16.263 1.436 19.823 sesameQC_plotBetaByDesign 16.140 1.260 17.464 KYCG_buildGeneDBs 16.796 0.570 18.395 KYCG_plotMetaEnrichment 16.645 0.696 18.541 sdf_read_table 16.165 0.614 18.141 visualizeGene 15.999 0.548 18.947 DMR 15.622 0.641 20.372 getSexInfo 14.653 0.583 17.504 deidentify 13.666 0.468 15.080 inferStrain 13.048 0.847 17.570 createUCSCtrack 11.366 0.432 14.693 dbStats 10.940 0.755 13.299 reIdentify 11.469 0.226 12.294 estimateLeukocyte 10.581 0.603 13.132 KYCG_plotSetEnrichment 10.260 0.598 11.535 dyeBiasCorrMostBalanced 10.027 0.343 11.388 openSesame 9.050 0.787 10.948 dyeBiasNL 9.161 0.496 11.186 testEnrichment 8.582 0.803 11.024 probeSuccessRate 8.722 0.460 14.126 inferSex 8.421 0.475 9.760 getMask 8.010 0.472 10.241 bisConversionControl 7.287 0.289 8.463 prepSesame 6.416 0.494 8.443 visualizeProbes 6.649 0.179 7.493 sdf_write_table 6.175 0.303 7.055 scrubSoft 5.210 0.796 6.239 parseGEOsignalMU 5.099 0.531 6.575 sesameQC_rankStats 5.185 0.371 6.213 totalIntensities 5.058 0.405 6.309 KYCG_plotWaterfall 5.165 0.286 5.849 inferSexKaryotypes 5.150 0.248 5.654 meanIntensity 4.700 0.638 5.984 updateSigDF 5.007 0.315 6.440 mapToMammal40 4.686 0.438 5.969 summaryExtractTest 4.188 0.815 6.230 detectionPnegEcdf 4.749 0.199 5.731 KYCG_getDBs 4.553 0.360 5.521 checkLevels 4.432 0.454 5.161 dyeBiasCorr 4.562 0.292 5.573 print.DMLSummary 4.102 0.735 5.981 qualityMask 4.259 0.506 6.074 predictAge 3.806 0.165 5.490 formatVCF 3.575 0.312 7.129 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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/4.3-x86_64/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 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (64-bit) 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, sort, 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 1 ] > > proc.time() user system elapsed 35.190 2.743 42.014
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0.000 | 0.000 | 0.001 | |
DML | 16.186 | 1.904 | 20.271 | |
DMLpredict | 2.375 | 0.198 | 2.981 | |
DMR | 15.622 | 0.641 | 20.372 | |
ELBAR | 21.638 | 2.889 | 26.531 | |
KYCG_annoProbes | 21.354 | 0.962 | 23.640 | |
KYCG_buildGeneDBs | 16.796 | 0.570 | 18.395 | |
KYCG_getDBs | 4.553 | 0.360 | 5.521 | |
KYCG_listDBGroups | 0.055 | 0.004 | 0.064 | |
KYCG_loadDBs | 0.000 | 0.001 | 0.002 | |
KYCG_plotBar | 0.405 | 0.049 | 0.493 | |
KYCG_plotDot | 1.472 | 0.154 | 1.773 | |
KYCG_plotEnrichAll | 29.298 | 1.327 | 33.564 | |
KYCG_plotLollipop | 0.371 | 0.024 | 0.424 | |
KYCG_plotManhattan | 1.371 | 0.150 | 1.636 | |
KYCG_plotMeta | 31.679 | 1.148 | 34.791 | |
KYCG_plotMetaEnrichment | 16.645 | 0.696 | 18.541 | |
KYCG_plotPointRange | 4.280 | 0.244 | 4.763 | |
KYCG_plotSetEnrichment | 10.260 | 0.598 | 11.535 | |
KYCG_plotVolcano | 0.301 | 0.006 | 0.319 | |
KYCG_plotWaterfall | 5.165 | 0.286 | 5.849 | |
MValueToBetaValue | 0.000 | 0.001 | 0.001 | |
SigDF | 0.521 | 0.073 | 0.681 | |
addMask | 0.131 | 0.001 | 0.133 | |
aggregateTestEnrichments | 4.243 | 0.070 | 4.415 | |
betasCollapseToPfx | 0.004 | 0.001 | 0.006 | |
bisConversionControl | 7.287 | 0.289 | 8.463 | |
calcEffectSize | 2.398 | 0.209 | 2.765 | |
checkLevels | 4.432 | 0.454 | 5.161 | |
cnSegmentation | 0.553 | 0.101 | 0.760 | |
compareMouseStrainReference | 29.187 | 0.574 | 32.156 | |
compareMouseTissueReference | 0.000 | 0.001 | 0.001 | |
compareReference | 26.708 | 0.864 | 30.145 | |
controls | 3.577 | 0.292 | 4.599 | |
convertTo | 20.615 | 0.607 | 23.651 | |
createUCSCtrack | 11.366 | 0.432 | 14.693 | |
dataFrame2sesameQC | 2.158 | 0.214 | 2.746 | |
dbStats | 10.940 | 0.755 | 13.299 | |
deidentify | 13.666 | 0.468 | 15.080 | |
detectionPnegEcdf | 4.749 | 0.199 | 5.731 | |
diffRefSet | 21.465 | 0.861 | 24.327 | |
dmContrasts | 2.971 | 0.212 | 3.548 | |
dyeBiasCorr | 4.562 | 0.292 | 5.573 | |
dyeBiasCorrMostBalanced | 10.027 | 0.343 | 11.388 | |
dyeBiasL | 3.087 | 0.158 | 4.998 | |
dyeBiasNL | 9.161 | 0.496 | 11.186 | |
estimateLeukocyte | 10.581 | 0.603 | 13.132 | |
formatVCF | 3.575 | 0.312 | 7.129 | |
getAFTypeIbySumAlleles | 2.923 | 0.257 | 4.597 | |
getAFs | 1.789 | 0.117 | 2.698 | |
getBetas | 1.423 | 0.132 | 3.294 | |
getMask | 8.010 | 0.472 | 10.241 | |
getRefSet | 19.236 | 0.683 | 21.924 | |
getSexInfo | 14.653 | 0.583 | 17.504 | |
imputeTo | 2.882 | 0.219 | 3.891 | |
inferEthnicity | 4.042 | 0.273 | 4.747 | |
inferInfiniumIChannel | 0.914 | 1.463 | 2.520 | |
inferSex | 8.421 | 0.475 | 9.760 | |
inferSexKaryotypes | 5.150 | 0.248 | 5.654 | |
inferSpecies | 24.557 | 1.002 | 28.703 | |
inferStrain | 13.048 | 0.847 | 17.570 | |
inferTissue | 16.263 | 1.436 | 19.823 | |
initFileSet | 2.084 | 0.284 | 2.834 | |
listAvailableMasks | 2.905 | 0.188 | 3.473 | |
mapFileSet | 0.059 | 0.005 | 0.065 | |
mapToMammal40 | 4.686 | 0.438 | 5.969 | |
matchDesign | 23.327 | 0.768 | 25.604 | |
meanIntensity | 4.700 | 0.638 | 5.984 | |
medianTotalIntensity | 1.432 | 0.100 | 2.231 | |
noMasked | 3.076 | 0.093 | 3.887 | |
noob | 3.551 | 0.539 | 4.257 | |
openSesame | 9.050 | 0.787 | 10.948 | |
openSesameToFile | 2.656 | 0.025 | 2.780 | |
pOOBAH | 2.355 | 0.017 | 2.613 | |
palgen | 0.069 | 0.011 | 0.082 | |
parseGEOsignalMU | 5.099 | 0.531 | 6.575 | |
predictAge | 3.806 | 0.165 | 5.490 | |
predictAgeHorvath353 | 0.001 | 0.000 | 0.000 | |
predictAgeSkinBlood | 0.001 | 0.000 | 0.001 | |
predictMouseAgeInMonth | 0.000 | 0.001 | 0.001 | |
prefixMask | 1.141 | 0.004 | 1.158 | |
prefixMaskButC | 0.315 | 0.002 | 0.320 | |
prefixMaskButCG | 0.126 | 0.001 | 0.129 | |
prepSesame | 6.416 | 0.494 | 8.443 | |
prepSesameList | 0.004 | 0.002 | 0.005 | |
print.DMLSummary | 4.102 | 0.735 | 5.981 | |
print.fileSet | 2.071 | 0.233 | 2.674 | |
probeID_designType | 0.000 | 0.001 | 0.001 | |
probeSuccessRate | 8.722 | 0.460 | 14.126 | |
qualityMask | 4.259 | 0.506 | 6.074 | |
reIdentify | 11.469 | 0.226 | 12.294 | |
readFileSet | 0.094 | 0.006 | 0.107 | |
readIDATpair | 0.227 | 0.004 | 0.237 | |
recommendedMaskNames | 0.000 | 0.001 | 0.002 | |
resetMask | 0.691 | 0.083 | 1.046 | |
scrub | 3.756 | 0.339 | 4.266 | |
scrubSoft | 5.210 | 0.796 | 6.239 | |
sdfPlatform | 0.547 | 0.090 | 0.942 | |
sdf_read_table | 16.165 | 0.614 | 18.141 | |
sdf_write_table | 6.175 | 0.303 | 7.055 | |
searchIDATprefixes | 0.007 | 0.005 | 0.013 | |
sesame-package | 3.845 | 0.397 | 4.400 | |
sesameAnno_buildAddressFile | 0.001 | 0.000 | 0.001 | |
sesameAnno_buildManifestGRanges | 0.000 | 0.001 | 0.001 | |
sesameAnno_download | 0.000 | 0.001 | 0.001 | |
sesameAnno_get | 0.001 | 0.001 | 0.001 | |
sesameAnno_readManifestTSV | 0.000 | 0.001 | 0.001 | |
sesameData_getAnno | 0 | 0 | 0 | |
sesameQC_calcStats | 36.198 | 1.715 | 38.584 | |
sesameQC_getStats | 3.445 | 0.018 | 3.502 | |
sesameQC_plotBar | 19.484 | 0.681 | 21.317 | |
sesameQC_plotBetaByDesign | 16.140 | 1.260 | 17.464 | |
sesameQC_plotHeatSNPs | 29.858 | 1.789 | 32.851 | |
sesameQC_plotIntensVsBetas | 2.920 | 0.354 | 3.877 | |
sesameQC_plotRedGrnQQ | 2.247 | 0.396 | 2.948 | |
sesameQC_rankStats | 5.185 | 0.371 | 6.213 | |
sesame_checkVersion | 0.006 | 0.001 | 0.008 | |
sesamize | 0.000 | 0.000 | 0.001 | |
setMask | 0.159 | 0.002 | 0.168 | |
signalMU | 1.541 | 0.188 | 2.200 | |
sliceFileSet | 0.061 | 0.005 | 0.068 | |
summaryExtractTest | 4.188 | 0.815 | 6.230 | |
testEnrichment | 8.582 | 0.803 | 11.024 | |
testEnrichmentGene | 175.584 | 7.063 | 202.861 | |
testEnrichmentSEA | 18.278 | 0.959 | 21.112 | |
totalIntensities | 5.058 | 0.405 | 6.309 | |
updateSigDF | 5.007 | 0.315 | 6.440 | |
visualizeGene | 15.999 | 0.548 | 18.947 | |
visualizeProbes | 6.649 | 0.179 | 7.493 | |
visualizeRegion | 1.153 | 0.020 | 1.190 | |
visualizeSegments | 2.548 | 0.894 | 4.090 | |