Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-18 11:47 -0400 (Fri, 18 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4474 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4733 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4479 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4509 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4457 |
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 1925/2273 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sesame 1.23.9 (landing page) Wanding Zhou
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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. |
Package: sesame |
Version: 1.23.9 |
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_1.23.9.tar.gz |
StartedAt: 2024-10-18 02:24:13 -0400 (Fri, 18 Oct 2024) |
EndedAt: 2024-10-18 02:39:06 -0400 (Fri, 18 Oct 2024) |
EllapsedTime: 893.5 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_1.23.9.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: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.23.9’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 32.059 2.314 34.485 imputeBetasByGenomicNeighbors 25.424 0.899 26.355 sesameQC_calcStats 17.229 1.082 18.338 KYCG_plotMeta 17.232 0.759 18.084 inferSex 16.158 0.731 16.907 ELBAR 13.680 2.416 16.153 KYCG_plotEnrichAll 14.127 1.026 15.221 imputeBetas 13.300 1.066 14.388 sesameQC_plotHeatSNPs 13.490 0.798 14.314 inferSpecies 10.180 0.443 10.642 sesameQC_plotBar 10.017 0.273 10.307 KYCG_annoProbes 9.562 0.522 10.124 KYCG_plotMetaEnrichment 9.432 0.555 10.050 sesameQC_plotBetaByDesign 8.908 0.892 9.812 diffRefSet 9.185 0.453 9.653 testEnrichmentSEA 8.585 0.854 9.463 compareMouseStrainReference 8.696 0.450 9.171 matchDesign 8.568 0.519 9.105 KYCG_buildGeneDBs 8.212 0.356 8.595 getRefSet 8.001 0.488 8.504 compareReference 8.060 0.408 8.488 visualizeGene 7.386 0.472 7.876 DML 6.639 0.786 7.452 estimateLeukocyte 5.959 0.595 6.574 sdf_read_table 6.284 0.232 6.530 DMR 5.965 0.200 6.184 inferTissue 5.188 0.968 6.165 inferStrain 5.626 0.409 6.041 dyeBiasNL 5.518 0.415 5.949 dbStats 4.871 0.499 5.376 * 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-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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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, 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 16.843 1.383 18.277
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0 | 0 | 0 | |
DML | 6.639 | 0.786 | 7.452 | |
DMLpredict | 0.918 | 0.067 | 0.989 | |
DMR | 5.965 | 0.200 | 6.184 | |
ELBAR | 13.680 | 2.416 | 16.153 | |
KYCG_annoProbes | 9.562 | 0.522 | 10.124 | |
KYCG_buildGeneDBs | 8.212 | 0.356 | 8.595 | |
KYCG_getDBs | 2.039 | 0.203 | 2.250 | |
KYCG_listDBGroups | 0.021 | 0.001 | 0.022 | |
KYCG_loadDBs | 0 | 0 | 0 | |
KYCG_plotBar | 0.146 | 0.013 | 0.159 | |
KYCG_plotDot | 0.510 | 0.023 | 0.535 | |
KYCG_plotEnrichAll | 14.127 | 1.026 | 15.221 | |
KYCG_plotLollipop | 0.125 | 0.003 | 0.129 | |
KYCG_plotManhattan | 1.079 | 0.150 | 1.231 | |
KYCG_plotMeta | 17.232 | 0.759 | 18.084 | |
KYCG_plotMetaEnrichment | 9.432 | 0.555 | 10.050 | |
KYCG_plotPointRange | 1.784 | 0.187 | 1.999 | |
KYCG_plotSetEnrichment | 4.057 | 0.432 | 4.508 | |
KYCG_plotVolcano | 0.105 | 0.001 | 0.107 | |
KYCG_plotWaterfall | 1.810 | 0.149 | 1.972 | |
MValueToBetaValue | 0.000 | 0.001 | 0.000 | |
SigDF | 0.211 | 0.030 | 0.242 | |
addMask | 0.188 | 0.021 | 0.209 | |
aggregateTestEnrichments | 1.378 | 0.118 | 1.499 | |
betasCollapseToPfx | 0.009 | 0.001 | 0.010 | |
bisConversionControl | 3.702 | 0.175 | 3.890 | |
calcEffectSize | 0.881 | 0.087 | 0.974 | |
checkLevels | 2.406 | 0.218 | 2.631 | |
cnSegmentation | 0.216 | 0.062 | 0.279 | |
compareMouseStrainReference | 8.696 | 0.450 | 9.171 | |
compareMouseTissueReference | 0.000 | 0.000 | 0.001 | |
compareReference | 8.060 | 0.408 | 8.488 | |
controls | 1.459 | 0.136 | 1.598 | |
createUCSCtrack | 4.229 | 0.262 | 4.502 | |
dbStats | 4.871 | 0.499 | 5.376 | |
deidentify | 4.014 | 0.260 | 4.283 | |
detectionPnegEcdf | 1.969 | 0.082 | 2.053 | |
diffRefSet | 9.185 | 0.453 | 9.653 | |
dmContrasts | 1.512 | 0.168 | 1.684 | |
dyeBiasCorr | 2.021 | 0.178 | 2.201 | |
dyeBiasCorrMostBalanced | 4.374 | 0.177 | 4.560 | |
dyeBiasL | 2.179 | 0.110 | 2.293 | |
dyeBiasNL | 5.518 | 0.415 | 5.949 | |
estimateLeukocyte | 5.959 | 0.595 | 6.574 | |
formatVCF | 1.529 | 0.170 | 1.706 | |
getAFTypeIbySumAlleles | 1.220 | 0.206 | 1.434 | |
getAFs | 0.797 | 0.097 | 0.894 | |
getBetas | 0.577 | 0.038 | 0.615 | |
getMask | 4.411 | 0.540 | 4.965 | |
getRefSet | 8.001 | 0.488 | 8.504 | |
imputeBetas | 13.300 | 1.066 | 14.388 | |
imputeBetasByGenomicNeighbors | 25.424 | 0.899 | 26.355 | |
imputeBetasMatrixByMean | 0.001 | 0.000 | 0.001 | |
inferEthnicity | 0.000 | 0.000 | 0.001 | |
inferInfiniumIChannel | 0.293 | 0.359 | 0.658 | |
inferSex | 16.158 | 0.731 | 16.907 | |
inferSpecies | 10.180 | 0.443 | 10.642 | |
inferStrain | 5.626 | 0.409 | 6.041 | |
inferTissue | 5.188 | 0.968 | 6.165 | |
initFileSet | 0.849 | 0.270 | 1.124 | |
listAvailableMasks | 0.920 | 0.228 | 1.150 | |
mLiftOver | 0.001 | 0.001 | 0.001 | |
mapFileSet | 0.027 | 0.007 | 0.035 | |
mapToMammal40 | 1.943 | 0.358 | 2.309 | |
matchDesign | 8.568 | 0.519 | 9.105 | |
meanIntensity | 1.875 | 0.124 | 2.002 | |
medianTotalIntensity | 0.632 | 0.035 | 0.669 | |
noMasked | 3.048 | 0.638 | 3.703 | |
noob | 1.527 | 0.019 | 1.551 | |
openSesame | 3.780 | 0.671 | 4.469 | |
openSesameToFile | 1.101 | 0.013 | 1.115 | |
pOOBAH | 1.072 | 0.003 | 1.076 | |
palgen | 0.035 | 0.006 | 0.043 | |
parseGEOsignalMU | 2.255 | 0.118 | 2.382 | |
predictAge | 1.860 | 0.489 | 2.357 | |
predictAgeHorvath353 | 0 | 0 | 0 | |
predictAgeSkinBlood | 0 | 0 | 0 | |
predictMouseAgeInMonth | 0.001 | 0.000 | 0.000 | |
prefixMask | 0.632 | 0.002 | 0.635 | |
prefixMaskButC | 0.174 | 0.001 | 0.174 | |
prefixMaskButCG | 0.070 | 0.000 | 0.071 | |
prepSesame | 2.834 | 0.129 | 2.973 | |
prepSesameList | 0.001 | 0.000 | 0.002 | |
print.DMLSummary | 2.369 | 0.541 | 2.914 | |
print.fileSet | 0.818 | 0.152 | 0.971 | |
probeID_designType | 0 | 0 | 0 | |
probeSuccessRate | 3.973 | 0.353 | 4.343 | |
qualityMask | 1.591 | 0.211 | 1.808 | |
reIdentify | 3.240 | 0.264 | 3.525 | |
readFileSet | 0.043 | 0.002 | 0.045 | |
readIDATpair | 0.096 | 0.001 | 0.098 | |
recommendedMaskNames | 0 | 0 | 0 | |
resetMask | 0.279 | 0.053 | 0.333 | |
scrub | 1.779 | 0.009 | 1.791 | |
scrubSoft | 2.611 | 0.624 | 3.238 | |
sdfPlatform | 0.200 | 0.036 | 0.236 | |
sdf_read_table | 6.284 | 0.232 | 6.530 | |
sdf_write_table | 1.817 | 0.073 | 1.891 | |
searchIDATprefixes | 0.003 | 0.002 | 0.005 | |
sesame-package | 1.492 | 0.087 | 1.584 | |
sesameAnno_attachManifest | 0 | 0 | 0 | |
sesameAnno_buildAddressFile | 0 | 0 | 0 | |
sesameAnno_buildManifestGRanges | 0 | 0 | 0 | |
sesameAnno_download | 0 | 0 | 0 | |
sesameAnno_readManifestTSV | 0 | 0 | 0 | |
sesameQC_calcStats | 17.229 | 1.082 | 18.338 | |
sesameQC_getStats | 1.764 | 0.162 | 1.929 | |
sesameQC_plotBar | 10.017 | 0.273 | 10.307 | |
sesameQC_plotBetaByDesign | 8.908 | 0.892 | 9.812 | |
sesameQC_plotHeatSNPs | 13.490 | 0.798 | 14.314 | |
sesameQC_plotIntensVsBetas | 1.592 | 0.162 | 1.756 | |
sesameQC_plotRedGrnQQ | 0.823 | 0.089 | 0.917 | |
sesameQC_rankStats | 2.691 | 0.222 | 2.917 | |
sesameQCtoDF | 1.765 | 0.041 | 1.808 | |
sesame_checkVersion | 0.003 | 0.001 | 0.004 | |
sesamize | 0.000 | 0.000 | 0.001 | |
setMask | 0.087 | 0.000 | 0.087 | |
signalMU | 0.826 | 0.070 | 0.904 | |
sliceFileSet | 0.033 | 0.007 | 0.040 | |
summaryExtractTest | 2.130 | 0.748 | 2.896 | |
testEnrichment | 4.132 | 0.606 | 4.750 | |
testEnrichmentGene | 32.059 | 2.314 | 34.485 | |
testEnrichmentSEA | 8.585 | 0.854 | 9.463 | |
totalIntensities | 2.234 | 0.171 | 2.411 | |
updateSigDF | 2.285 | 0.301 | 2.593 | |
visualizeGene | 7.386 | 0.472 | 7.876 | |
visualizeProbes | 0.767 | 0.002 | 0.770 | |
visualizeRegion | 0.276 | 0.002 | 0.278 | |
visualizeSegments | 1.769 | 0.498 | 2.276 | |