Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-02-13 12:13 -0500 (Thu, 13 Feb 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4754 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4502 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4525 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4477 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4414 |
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 1938/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sesame 1.24.0 (landing page) Wanding Zhou
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: sesame |
Version: 1.24.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sesame_1.24.0.tar.gz |
StartedAt: 2025-02-11 10:23:16 -0000 (Tue, 11 Feb 2025) |
EndedAt: 2025-02-11 10:39:04 -0000 (Tue, 11 Feb 2025) |
EllapsedTime: 947.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sesame.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sesame_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403) * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.24.0’ * 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 43.141 0.721 43.994 imputeBetasByGenomicNeighbors 38.995 0.539 39.834 inferSex 25.655 0.239 25.937 imputeBetas 23.199 0.407 23.861 sesameQC_plotHeatSNPs 23.130 0.268 23.444 sesameQC_calcStats 23.128 0.147 23.312 KYCG_plotMeta 22.988 0.148 23.244 KYCG_plotEnrichAll 20.366 0.562 21.023 ELBAR 16.620 0.268 16.964 matchDesign 16.194 0.255 16.481 compareMouseStrainReference 15.551 0.108 15.699 inferSpecies 15.132 0.368 15.531 diffRefSet 13.982 0.195 14.437 KYCG_annoProbes 13.999 0.175 14.325 compareReference 13.931 0.199 14.161 sesameQC_plotBetaByDesign 12.773 0.040 12.840 KYCG_plotMetaEnrichment 12.099 0.187 12.322 sesameQC_plotBar 11.872 0.144 12.047 getRefSet 11.652 0.148 11.830 testEnrichmentSEA 11.626 0.160 11.812 KYCG_buildGeneDBs 10.625 0.211 10.869 visualizeGene 9.455 0.108 9.587 DML 9.133 0.351 9.599 DMR 9.029 0.310 9.526 inferStrain 8.623 0.243 8.895 sdf_read_table 8.167 0.124 8.303 inferTissue 7.650 0.156 7.823 KYCG_plotSetEnrichment 7.460 0.096 7.581 dyeBiasNL 6.986 0.100 7.114 dbStats 6.947 0.124 7.120 estimateLeukocyte 6.820 0.215 7.061 getMask 6.638 0.139 6.805 deidentify 6.488 0.087 6.612 dyeBiasCorrMostBalanced 6.130 0.191 6.347 bisConversionControl 6.024 0.107 6.155 createUCSCtrack 6.040 0.076 6.129 openSesame 5.709 0.227 5.973 reIdentify 5.615 0.028 5.653 testEnrichment 5.417 0.132 5.560 probeSuccessRate 5.400 0.084 5.494 * 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/bin/R CMD INSTALL sesame ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.2/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 4.4.2 (2024-10-31) -- "Pile of Leaves" 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, saveRDS, 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 20.579 0.695 21.310
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0 | 0 | 0 | |
DML | 9.133 | 0.351 | 9.599 | |
DMLpredict | 1.471 | 0.027 | 1.506 | |
DMR | 9.029 | 0.310 | 9.526 | |
ELBAR | 16.620 | 0.268 | 16.964 | |
KYCG_annoProbes | 13.999 | 0.175 | 14.325 | |
KYCG_buildGeneDBs | 10.625 | 0.211 | 10.869 | |
KYCG_getDBs | 3.061 | 0.095 | 3.169 | |
KYCG_listDBGroups | 0.039 | 0.000 | 0.039 | |
KYCG_loadDBs | 0 | 0 | 0 | |
KYCG_plotBar | 0.245 | 0.024 | 0.270 | |
KYCG_plotDot | 0.919 | 0.020 | 0.941 | |
KYCG_plotEnrichAll | 20.366 | 0.562 | 21.023 | |
KYCG_plotLollipop | 0.211 | 0.000 | 0.212 | |
KYCG_plotManhattan | 1.335 | 0.000 | 1.338 | |
KYCG_plotMeta | 22.988 | 0.148 | 23.244 | |
KYCG_plotMetaEnrichment | 12.099 | 0.187 | 12.322 | |
KYCG_plotPointRange | 2.480 | 0.064 | 2.557 | |
KYCG_plotSetEnrichment | 7.460 | 0.096 | 7.581 | |
KYCG_plotVolcano | 0.198 | 0.000 | 0.198 | |
KYCG_plotWaterfall | 3.123 | 0.028 | 3.161 | |
MValueToBetaValue | 0 | 0 | 0 | |
SigDF | 0.371 | 0.020 | 0.392 | |
addMask | 0.112 | 0.000 | 0.112 | |
aggregateTestEnrichments | 2.460 | 0.040 | 2.506 | |
betasCollapseToPfx | 0.018 | 0.000 | 0.017 | |
bisConversionControl | 6.024 | 0.107 | 6.155 | |
calcEffectSize | 1.312 | 0.024 | 1.339 | |
checkLevels | 3.181 | 0.072 | 3.263 | |
cnSegmentation | 0.363 | 0.004 | 0.368 | |
compareMouseStrainReference | 15.551 | 0.108 | 15.699 | |
compareMouseTissueReference | 0.001 | 0.000 | 0.000 | |
compareReference | 13.931 | 0.199 | 14.161 | |
controls | 2.149 | 0.064 | 2.217 | |
createUCSCtrack | 6.040 | 0.076 | 6.129 | |
dbStats | 6.947 | 0.124 | 7.120 | |
deidentify | 6.488 | 0.087 | 6.612 | |
detectionPnegEcdf | 2.825 | 0.040 | 2.947 | |
diffRefSet | 13.982 | 0.195 | 14.437 | |
dmContrasts | 2.114 | 0.040 | 2.161 | |
dyeBiasCorr | 3.063 | 0.060 | 3.132 | |
dyeBiasCorrMostBalanced | 6.130 | 0.191 | 6.347 | |
dyeBiasL | 3.194 | 0.052 | 3.253 | |
dyeBiasNL | 6.986 | 0.100 | 7.114 | |
estimateLeukocyte | 6.820 | 0.215 | 7.061 | |
formatVCF | 2.195 | 0.056 | 2.257 | |
getAFTypeIbySumAlleles | 1.928 | 0.048 | 1.983 | |
getAFs | 1.292 | 0.016 | 1.312 | |
getBetas | 1.015 | 0.016 | 1.033 | |
getMask | 6.638 | 0.139 | 6.805 | |
getRefSet | 11.652 | 0.148 | 11.830 | |
imputeBetas | 23.199 | 0.407 | 23.861 | |
imputeBetasByGenomicNeighbors | 38.995 | 0.539 | 39.834 | |
imputeBetasMatrixByMean | 0.001 | 0.000 | 0.002 | |
inferEthnicity | 0.001 | 0.000 | 0.001 | |
inferInfiniumIChannel | 0.306 | 0.096 | 0.401 | |
inferSex | 25.655 | 0.239 | 25.937 | |
inferSpecies | 15.132 | 0.368 | 15.531 | |
inferStrain | 8.623 | 0.243 | 8.895 | |
inferTissue | 7.650 | 0.156 | 7.823 | |
initFileSet | 1.229 | 0.040 | 1.271 | |
listAvailableMasks | 1.322 | 0.023 | 1.350 | |
mLiftOver | 0.001 | 0.000 | 0.000 | |
mapFileSet | 0.04 | 0.00 | 0.04 | |
mapToMammal40 | 2.757 | 0.080 | 2.848 | |
matchDesign | 16.194 | 0.255 | 16.481 | |
meanIntensity | 2.758 | 0.084 | 2.850 | |
medianTotalIntensity | 0.832 | 0.095 | 0.930 | |
noMasked | 3.727 | 0.068 | 3.802 | |
noob | 2.309 | 0.048 | 2.361 | |
openSesame | 5.709 | 0.227 | 5.973 | |
openSesameToFile | 1.641 | 0.008 | 1.659 | |
pOOBAH | 1.369 | 0.000 | 1.371 | |
palgen | 0.048 | 0.000 | 0.052 | |
parseGEOsignalMU | 3.102 | 0.044 | 3.152 | |
predictAge | 2.245 | 0.032 | 2.280 | |
predictAgeHorvath353 | 0 | 0 | 0 | |
predictAgeSkinBlood | 0 | 0 | 0 | |
predictMouseAgeInMonth | 0.001 | 0.000 | 0.000 | |
prefixMask | 0.515 | 0.000 | 0.515 | |
prefixMaskButC | 0.155 | 0.000 | 0.156 | |
prefixMaskButCG | 0.065 | 0.000 | 0.066 | |
prepSesame | 4.079 | 0.052 | 4.140 | |
prepSesameList | 0.001 | 0.000 | 0.001 | |
print.DMLSummary | 3.290 | 0.120 | 3.416 | |
print.fileSet | 1.279 | 0.032 | 1.314 | |
probeID_designType | 0.001 | 0.000 | 0.000 | |
probeSuccessRate | 5.400 | 0.084 | 5.494 | |
qualityMask | 2.400 | 0.059 | 2.465 | |
reIdentify | 5.615 | 0.028 | 5.653 | |
readFileSet | 0.058 | 0.000 | 0.058 | |
readIDATpair | 0.126 | 0.000 | 0.126 | |
recommendedMaskNames | 0 | 0 | 0 | |
resetMask | 0.539 | 0.008 | 0.548 | |
scrub | 2.843 | 0.072 | 2.918 | |
scrubSoft | 4.381 | 0.016 | 4.404 | |
sdfPlatform | 0.339 | 0.024 | 0.364 | |
sdf_read_table | 8.167 | 0.124 | 8.303 | |
sdf_write_table | 2.285 | 0.060 | 2.402 | |
searchIDATprefixes | 0.005 | 0.000 | 0.009 | |
sesame-package | 2.223 | 0.060 | 2.291 | |
sesameAnno_attachManifest | 0 | 0 | 0 | |
sesameAnno_buildAddressFile | 0 | 0 | 0 | |
sesameAnno_buildManifestGRanges | 0 | 0 | 0 | |
sesameAnno_download | 0.001 | 0.000 | 0.000 | |
sesameAnno_readManifestTSV | 0 | 0 | 0 | |
sesameQC_calcStats | 23.128 | 0.147 | 23.312 | |
sesameQC_getStats | 1.938 | 0.004 | 1.944 | |
sesameQC_plotBar | 11.872 | 0.144 | 12.047 | |
sesameQC_plotBetaByDesign | 12.773 | 0.040 | 12.840 | |
sesameQC_plotHeatSNPs | 23.130 | 0.268 | 23.444 | |
sesameQC_plotIntensVsBetas | 2.284 | 0.032 | 2.320 | |
sesameQC_plotRedGrnQQ | 1.533 | 0.035 | 1.572 | |
sesameQC_rankStats | 4.077 | 0.060 | 4.149 | |
sesameQCtoDF | 1.918 | 0.008 | 1.929 | |
sesame_checkVersion | 0.001 | 0.004 | 0.004 | |
sesamize | 0.001 | 0.000 | 0.000 | |
setMask | 0.106 | 0.000 | 0.106 | |
signalMU | 1.104 | 0.040 | 1.147 | |
sliceFileSet | 0.037 | 0.000 | 0.038 | |
summaryExtractTest | 2.728 | 0.152 | 2.886 | |
testEnrichment | 5.417 | 0.132 | 5.560 | |
testEnrichmentGene | 43.141 | 0.721 | 43.994 | |
testEnrichmentSEA | 11.626 | 0.160 | 11.812 | |
totalIntensities | 3.110 | 0.092 | 3.210 | |
updateSigDF | 3.775 | 0.143 | 3.931 | |
visualizeGene | 9.455 | 0.108 | 9.587 | |
visualizeProbes | 3.566 | 0.020 | 3.595 | |
visualizeRegion | 0.450 | 0.000 | 0.452 | |
visualizeSegments | 2.023 | 0.068 | 2.097 | |