Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:45 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the sesame package: - 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: 1.22.0 |
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_1.22.0.tar.gz |
StartedAt: 2024-05-07 00:54:35 -0400 (Tue, 07 May 2024) |
EndedAt: 2024-05-07 01:00:12 -0400 (Tue, 07 May 2024) |
EllapsedTime: 337.8 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_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/sesame.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘1.22.0’ * 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 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 41.427 1.609 44.277 inferSex 13.673 0.472 14.373 sesameQC_calcStats 8.004 0.571 8.630 KYCG_plotMeta 7.640 0.330 8.150 sesameQC_plotHeatSNPs 6.823 0.536 7.424 KYCG_plotEnrichAll 6.760 0.319 7.586 sesameQC_plotBar 6.112 0.181 6.411 inferSpecies 5.772 0.271 6.226 ELBAR 4.700 0.781 5.608 diffRefSet 4.961 0.251 5.329 KYCG_annoProbes 4.940 0.187 5.297 KYCG_buildGeneDBs 4.851 0.175 5.139 * 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 4.4.0 (2024-04-24) -- "Puppy Cup" 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': anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, 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 7.748 0.432 8.459
sesame.Rcheck/sesame-Ex.timings
name | user | system | elapsed | |
BetaValueToMValue | 0 | 0 | 0 | |
DML | 2.309 | 0.286 | 2.833 | |
DMLpredict | 0.337 | 0.028 | 0.421 | |
DMR | 2.549 | 0.074 | 2.736 | |
ELBAR | 4.700 | 0.781 | 5.608 | |
KYCG_annoProbes | 4.940 | 0.187 | 5.297 | |
KYCG_buildGeneDBs | 4.851 | 0.175 | 5.139 | |
KYCG_getDBs | 0.986 | 0.139 | 1.235 | |
KYCG_listDBGroups | 0.011 | 0.001 | 0.012 | |
KYCG_loadDBs | 0 | 0 | 0 | |
KYCG_plotBar | 0.066 | 0.008 | 0.075 | |
KYCG_plotDot | 0.213 | 0.016 | 0.229 | |
KYCG_plotEnrichAll | 6.760 | 0.319 | 7.586 | |
KYCG_plotLollipop | 0.047 | 0.004 | 0.051 | |
KYCG_plotManhattan | 0.578 | 0.031 | 0.610 | |
KYCG_plotMeta | 7.64 | 0.33 | 8.15 | |
KYCG_plotMetaEnrichment | 4.100 | 0.193 | 4.470 | |
KYCG_plotPointRange | 0.655 | 0.052 | 0.765 | |
KYCG_plotSetEnrichment | 1.838 | 0.157 | 2.106 | |
KYCG_plotVolcano | 0.043 | 0.001 | 0.044 | |
KYCG_plotWaterfall | 1.230 | 0.069 | 1.354 | |
MValueToBetaValue | 0 | 0 | 0 | |
SigDF | 0.082 | 0.020 | 0.157 | |
addMask | 0.016 | 0.000 | 0.017 | |
aggregateTestEnrichments | 0.357 | 0.035 | 0.396 | |
betasCollapseToPfx | 0.004 | 0.000 | 0.003 | |
bisConversionControl | 2.281 | 0.084 | 2.487 | |
calcEffectSize | 0.350 | 0.039 | 0.447 | |
checkLevels | 1.113 | 0.107 | 1.288 | |
cnSegmentation | 0.089 | 0.014 | 0.160 | |
compareMouseStrainReference | 3.551 | 0.152 | 3.820 | |
compareMouseTissueReference | 0.000 | 0.000 | 0.001 | |
compareReference | 3.818 | 0.146 | 4.080 | |
controls | 0.689 | 0.096 | 0.898 | |
createUCSCtrack | 2.021 | 0.124 | 2.260 | |
dataFrame2sesameQC | 0.277 | 0.035 | 0.368 | |
dbStats | 1.993 | 0.176 | 2.277 | |
deidentify | 1.659 | 0.161 | 1.935 | |
detectionPnegEcdf | 0.980 | 0.057 | 1.104 | |
diffRefSet | 4.961 | 0.251 | 5.329 | |
dmContrasts | 0.662 | 0.027 | 0.751 | |
dyeBiasCorr | 0.856 | 0.111 | 1.124 | |
dyeBiasCorrMostBalanced | 2.744 | 0.096 | 2.996 | |
dyeBiasL | 0.876 | 0.041 | 0.972 | |
dyeBiasNL | 2.218 | 0.114 | 2.389 | |
estimateLeukocyte | 2.293 | 0.121 | 2.528 | |
formatVCF | 0.708 | 0.052 | 0.872 | |
getAFTypeIbySumAlleles | 0.470 | 0.064 | 0.645 | |
getAFs | 0.381 | 0.035 | 0.473 | |
getBetas | 0.251 | 0.020 | 0.325 | |
getMask | 1.642 | 0.128 | 1.937 | |
getRefSet | 4.336 | 0.159 | 4.610 | |
imputeBetasMatrixByMean | 0.001 | 0.000 | 0.000 | |
inferEthnicity | 0.604 | 0.031 | 0.691 | |
inferInfiniumIChannel | 0.139 | 0.146 | 0.287 | |
inferSex | 13.673 | 0.472 | 14.373 | |
inferSpecies | 5.772 | 0.271 | 6.226 | |
inferStrain | 2.769 | 0.221 | 3.121 | |
inferTissue | 2.093 | 0.226 | 2.457 | |
initFileSet | 0.368 | 0.070 | 0.495 | |
listAvailableMasks | 0.582 | 0.081 | 0.726 | |
mLiftOver | 0 | 0 | 0 | |
mapFileSet | 0.016 | 0.000 | 0.017 | |
mapToMammal40 | 0.842 | 0.167 | 1.123 | |
matchDesign | 4.533 | 0.188 | 4.780 | |
meanIntensity | 0.925 | 0.106 | 1.183 | |
medianTotalIntensity | 0.266 | 0.044 | 0.368 | |
noMasked | 0.652 | 0.035 | 0.747 | |
noob | 0.840 | 0.120 | 0.959 | |
openSesame | 1.577 | 0.128 | 1.817 | |
openSesameToFile | 0.530 | 0.033 | 0.564 | |
pOOBAH | 0.534 | 0.023 | 0.558 | |
palgen | 0.015 | 0.003 | 0.018 | |
parseGEOsignalMU | 1.244 | 0.079 | 1.379 | |
predictAge | 0.849 | 0.043 | 0.947 | |
predictAgeHorvath353 | 0 | 0 | 0 | |
predictAgeSkinBlood | 0.000 | 0.001 | 0.000 | |
predictMouseAgeInMonth | 0 | 0 | 0 | |
prefixMask | 0.198 | 0.002 | 0.200 | |
prefixMaskButC | 0.053 | 0.001 | 0.054 | |
prefixMaskButCG | 0.018 | 0.001 | 0.019 | |
prepSesame | 1.514 | 0.143 | 1.713 | |
prepSesameList | 0.005 | 0.000 | 0.006 | |
print.DMLSummary | 1.037 | 0.105 | 1.261 | |
print.fileSet | 0.311 | 0.029 | 0.399 | |
probeID_designType | 0 | 0 | 0 | |
probeSuccessRate | 1.684 | 0.189 | 2.045 | |
qualityMask | 0.742 | 0.077 | 0.934 | |
reIdentify | 1.446 | 0.072 | 1.574 | |
readFileSet | 0.026 | 0.001 | 0.028 | |
readIDATpair | 0.047 | 0.004 | 0.052 | |
recommendedMaskNames | 0 | 0 | 0 | |
resetMask | 0.114 | 0.014 | 0.182 | |
scrub | 0.930 | 0.136 | 1.066 | |
scrubSoft | 1.350 | 0.217 | 1.573 | |
sdfPlatform | 0.120 | 0.041 | 0.218 | |
sdf_read_table | 3.188 | 0.178 | 3.480 | |
sdf_write_table | 0.908 | 0.043 | 1.015 | |
searchIDATprefixes | 0.001 | 0.001 | 0.004 | |
sesame-package | 0.858 | 0.068 | 0.981 | |
sesameAnno_buildAddressFile | 0 | 0 | 0 | |
sesameAnno_buildManifestGRanges | 0.000 | 0.001 | 0.000 | |
sesameAnno_download | 0 | 0 | 0 | |
sesameAnno_get | 0 | 0 | 0 | |
sesameAnno_readManifestTSV | 0 | 0 | 0 | |
sesameData_getAnno | 0 | 0 | 0 | |
sesameQC_calcStats | 8.004 | 0.571 | 8.630 | |
sesameQC_getStats | 0.853 | 0.027 | 0.879 | |
sesameQC_plotBar | 6.112 | 0.181 | 6.411 | |
sesameQC_plotBetaByDesign | 3.515 | 0.502 | 4.025 | |
sesameQC_plotHeatSNPs | 6.823 | 0.536 | 7.424 | |
sesameQC_plotIntensVsBetas | 1.361 | 0.156 | 1.575 | |
sesameQC_plotRedGrnQQ | 0.426 | 0.053 | 0.535 | |
sesameQC_rankStats | 1.114 | 0.179 | 1.404 | |
sesame_checkVersion | 0.001 | 0.000 | 0.001 | |
sesamize | 0 | 0 | 0 | |
setMask | 0.025 | 0.001 | 0.025 | |
signalMU | 0.244 | 0.036 | 0.349 | |
sliceFileSet | 0.015 | 0.001 | 0.016 | |
summaryExtractTest | 1.006 | 0.110 | 1.237 | |
testEnrichment | 1.818 | 0.250 | 2.255 | |
testEnrichmentGene | 41.427 | 1.609 | 44.277 | |
testEnrichmentSEA | 3.538 | 0.306 | 4.029 | |
totalIntensities | 0.939 | 0.062 | 1.117 | |
updateSigDF | 0.890 | 0.074 | 1.093 | |
visualizeGene | 4.629 | 0.177 | 4.981 | |
visualizeProbes | 0.281 | 0.005 | 0.287 | |
visualizeRegion | 0.223 | 0.008 | 0.231 | |
visualizeSegments | 0.818 | 0.143 | 1.017 | |