Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:41:07 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 1952/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sesame 1.22.0 (landing page) Wanding Zhou
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
kjohnson3 | macOS 13.6.5 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: sesame |
Version: 1.22.0 |
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings sesame_1.22.0.tar.gz |
StartedAt: 2024-05-04 11:57:21 -0000 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 12:18:46 -0000 (Sat, 04 May 2024) |
EllapsedTime: 1285.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sesame.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings sesame_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.22.0’ * 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 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 testEnrichmentGene 125.696 1.832 149.358 inferSex 43.881 0.902 49.188 sesameQC_calcStats 29.761 0.136 33.027 KYCG_plotMeta 26.035 0.493 29.855 sesameQC_plotHeatSNPs 25.914 0.136 27.690 ELBAR 23.137 0.466 24.815 KYCG_plotEnrichAll 21.684 1.106 30.403 sesameQC_plotBetaByDesign 18.398 0.184 18.616 matchDesign 17.454 0.284 18.850 inferSpecies 17.077 0.658 21.007 compareMouseStrainReference 16.690 0.343 19.238 KYCG_annoProbes 16.633 0.339 20.323 diffRefSet 16.030 0.300 18.511 compareReference 15.205 0.219 17.607 KYCG_plotMetaEnrichment 13.762 0.463 17.501 getRefSet 12.982 0.427 15.596 sesameQC_plotBar 12.967 0.147 15.304 testEnrichmentSEA 12.767 0.132 16.369 KYCG_buildGeneDBs 11.943 0.367 14.695 visualizeGene 11.256 0.188 14.889 DMR 10.997 0.379 13.755 inferStrain 10.442 0.256 12.869 DML 9.007 1.506 12.904 dyeBiasNL 9.773 0.088 10.955 dbStats 9.499 0.184 11.872 sdf_read_table 8.793 0.128 11.300 inferTissue 8.457 0.135 10.757 estimateLeukocyte 7.664 0.431 10.290 KYCG_plotSetEnrichment 7.759 0.151 10.092 deidentify 7.661 0.159 9.994 createUCSCtrack 7.042 0.112 9.321 openSesame 6.886 0.184 9.247 probeSuccessRate 6.548 0.104 9.905 scrubSoft 6.487 0.039 6.538 dyeBiasCorrMostBalanced 6.252 0.124 8.646 testEnrichment 6.213 0.148 10.794 reIdentify 6.152 0.056 7.397 getMask 5.702 0.275 9.241 sesameQC_rankStats 5.600 0.068 7.837 bisConversionControl 5.019 0.096 7.278 prepSesame 4.807 0.071 5.969 checkLevels 4.094 0.140 5.325 print.DMLSummary 3.754 0.144 6.059 totalIntensities 3.613 0.064 6.845 mapToMammal40 3.534 0.088 5.796 dyeBiasCorr 3.472 0.096 5.941 qualityMask 3.297 0.068 5.518 meanIntensity 3.255 0.100 5.510 summaryExtractTest 3.263 0.079 13.745 updateSigDF 3.220 0.083 5.485 KYCG_getDBs 3.191 0.099 5.444 KYCG_plotPointRange 2.790 0.072 5.545 * 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-beta-2024-04-15_r86425/bin/R CMD INSTALL sesame ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 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 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 22.809 2.204 27.197
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0.000 | 0.000 | 0.001 | |
DML | 9.007 | 1.506 | 12.904 | |
DMLpredict | 1.473 | 0.060 | 2.607 | |
DMR | 10.997 | 0.379 | 13.755 | |
ELBAR | 23.137 | 0.466 | 24.815 | |
KYCG_annoProbes | 16.633 | 0.339 | 20.323 | |
KYCG_buildGeneDBs | 11.943 | 0.367 | 14.695 | |
KYCG_getDBs | 3.191 | 0.099 | 5.444 | |
KYCG_listDBGroups | 0.034 | 0.000 | 0.035 | |
KYCG_loadDBs | 0 | 0 | 0 | |
KYCG_plotBar | 0.235 | 0.020 | 0.256 | |
KYCG_plotDot | 0.409 | 0.052 | 0.462 | |
KYCG_plotEnrichAll | 21.684 | 1.106 | 30.403 | |
KYCG_plotLollipop | 0.230 | 0.011 | 0.242 | |
KYCG_plotManhattan | 1.787 | 0.108 | 1.898 | |
KYCG_plotMeta | 26.035 | 0.493 | 29.855 | |
KYCG_plotMetaEnrichment | 13.762 | 0.463 | 17.501 | |
KYCG_plotPointRange | 2.790 | 0.072 | 5.545 | |
KYCG_plotSetEnrichment | 7.759 | 0.151 | 10.092 | |
KYCG_plotVolcano | 0.192 | 0.000 | 0.192 | |
KYCG_plotWaterfall | 3.367 | 0.108 | 4.560 | |
MValueToBetaValue | 0.000 | 0.000 | 0.001 | |
SigDF | 0.357 | 0.016 | 1.445 | |
addMask | 0.120 | 0.000 | 0.119 | |
aggregateTestEnrichments | 4.179 | 0.120 | 4.307 | |
betasCollapseToPfx | 0.012 | 0.004 | 0.016 | |
bisConversionControl | 5.019 | 0.096 | 7.278 | |
calcEffectSize | 1.460 | 0.067 | 2.616 | |
checkLevels | 4.094 | 0.140 | 5.325 | |
cnSegmentation | 0.366 | 0.024 | 1.464 | |
compareMouseStrainReference | 16.690 | 0.343 | 19.238 | |
compareMouseTissueReference | 0 | 0 | 0 | |
compareReference | 15.205 | 0.219 | 17.607 | |
controls | 2.380 | 0.060 | 4.588 | |
createUCSCtrack | 7.042 | 0.112 | 9.321 | |
dataFrame2sesameQC | 1.346 | 0.032 | 2.455 | |
dbStats | 9.499 | 0.184 | 11.872 | |
deidentify | 7.661 | 0.159 | 9.994 | |
detectionPnegEcdf | 3.273 | 0.052 | 4.404 | |
diffRefSet | 16.030 | 0.300 | 18.511 | |
dmContrasts | 2.407 | 0.039 | 3.531 | |
dyeBiasCorr | 3.472 | 0.096 | 5.941 | |
dyeBiasCorrMostBalanced | 6.252 | 0.124 | 8.646 | |
dyeBiasL | 3.752 | 0.108 | 4.948 | |
dyeBiasNL | 9.773 | 0.088 | 10.955 | |
estimateLeukocyte | 7.664 | 0.431 | 10.290 | |
formatVCF | 2.422 | 0.147 | 4.721 | |
getAFTypeIbySumAlleles | 2.302 | 0.116 | 4.591 | |
getAFs | 1.670 | 0.104 | 2.857 | |
getBetas | 1.228 | 0.040 | 2.344 | |
getMask | 5.702 | 0.275 | 9.241 | |
getRefSet | 12.982 | 0.427 | 15.596 | |
imputeBetasMatrixByMean | 0.003 | 0.000 | 0.003 | |
inferEthnicity | 1.952 | 0.064 | 3.096 | |
inferInfiniumIChannel | 0.355 | 0.084 | 0.439 | |
inferSex | 43.881 | 0.902 | 49.188 | |
inferSpecies | 17.077 | 0.658 | 21.007 | |
inferStrain | 10.442 | 0.256 | 12.869 | |
inferTissue | 8.457 | 0.135 | 10.757 | |
initFileSet | 1.361 | 0.028 | 2.467 | |
listAvailableMasks | 1.933 | 0.044 | 3.052 | |
mLiftOver | 0 | 0 | 0 | |
mapFileSet | 0.037 | 0.000 | 0.038 | |
mapToMammal40 | 3.534 | 0.088 | 5.796 | |
matchDesign | 17.454 | 0.284 | 18.850 | |
meanIntensity | 3.255 | 0.100 | 5.510 | |
medianTotalIntensity | 1.293 | 0.067 | 2.432 | |
noMasked | 2.517 | 0.040 | 3.641 | |
noob | 3.497 | 0.064 | 3.567 | |
openSesame | 6.886 | 0.184 | 9.247 | |
openSesameToFile | 1.914 | 0.032 | 1.950 | |
pOOBAH | 1.703 | 0.012 | 1.718 | |
palgen | 0.045 | 0.000 | 0.049 | |
parseGEOsignalMU | 3.773 | 0.036 | 4.888 | |
predictAge | 2.446 | 0.044 | 4.143 | |
predictAgeHorvath353 | 0.000 | 0.000 | 0.001 | |
predictAgeSkinBlood | 0 | 0 | 0 | |
predictMouseAgeInMonth | 0 | 0 | 0 | |
prefixMask | 0.536 | 0.000 | 0.537 | |
prefixMaskButC | 0.157 | 0.000 | 0.157 | |
prefixMaskButCG | 0.071 | 0.000 | 0.072 | |
prepSesame | 4.807 | 0.071 | 5.969 | |
prepSesameList | 0.002 | 0.000 | 0.002 | |
print.DMLSummary | 3.754 | 0.144 | 6.059 | |
print.fileSet | 1.349 | 0.036 | 2.459 | |
probeID_designType | 0 | 0 | 0 | |
probeSuccessRate | 6.548 | 0.104 | 9.905 | |
qualityMask | 3.297 | 0.068 | 5.518 | |
reIdentify | 6.152 | 0.056 | 7.397 | |
readFileSet | 0.056 | 0.003 | 0.059 | |
readIDATpair | 0.162 | 0.003 | 0.165 | |
recommendedMaskNames | 0 | 0 | 0 | |
resetMask | 0.487 | 0.016 | 1.575 | |
scrub | 4.197 | 0.111 | 4.316 | |
scrubSoft | 6.487 | 0.039 | 6.538 | |
sdfPlatform | 0.349 | 0.016 | 1.431 | |
sdf_read_table | 8.793 | 0.128 | 11.300 | |
sdf_write_table | 2.107 | 0.064 | 3.291 | |
searchIDATprefixes | 0.000 | 0.005 | 0.007 | |
sesame-package | 2.299 | 0.041 | 3.432 | |
sesameAnno_buildAddressFile | 0 | 0 | 0 | |
sesameAnno_buildManifestGRanges | 0 | 0 | 0 | |
sesameAnno_download | 0 | 0 | 0 | |
sesameAnno_get | 0.001 | 0.000 | 0.000 | |
sesameAnno_readManifestTSV | 0 | 0 | 0 | |
sesameData_getAnno | 0 | 0 | 0 | |
sesameQC_calcStats | 29.761 | 0.136 | 33.027 | |
sesameQC_getStats | 2.346 | 0.004 | 2.353 | |
sesameQC_plotBar | 12.967 | 0.147 | 15.304 | |
sesameQC_plotBetaByDesign | 18.398 | 0.184 | 18.616 | |
sesameQC_plotHeatSNPs | 25.914 | 0.136 | 27.690 | |
sesameQC_plotIntensVsBetas | 3.381 | 0.051 | 4.514 | |
sesameQC_plotRedGrnQQ | 2.103 | 0.040 | 3.222 | |
sesameQC_rankStats | 5.600 | 0.068 | 7.837 | |
sesame_checkVersion | 0.004 | 0.000 | 0.004 | |
sesamize | 0.000 | 0.000 | 0.001 | |
setMask | 0.147 | 0.000 | 0.148 | |
signalMU | 1.465 | 0.052 | 2.593 | |
sliceFileSet | 0.029 | 0.005 | 0.033 | |
summaryExtractTest | 3.263 | 0.079 | 13.745 | |
testEnrichment | 6.213 | 0.148 | 10.794 | |
testEnrichmentGene | 125.696 | 1.832 | 149.358 | |
testEnrichmentSEA | 12.767 | 0.132 | 16.369 | |
totalIntensities | 3.613 | 0.064 | 6.845 | |
updateSigDF | 3.220 | 0.083 | 5.485 | |
visualizeGene | 11.256 | 0.188 | 14.889 | |
visualizeProbes | 1.251 | 0.020 | 1.273 | |
visualizeRegion | 0.449 | 0.000 | 0.449 | |
visualizeSegments | 2.075 | 0.024 | 3.176 | |