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This page was generated on 2024-10-18 20:41 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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 1952/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.22.2  (landing page)
Wanding Zhou
Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_19
git_last_commit: 94fbff1
git_last_commit_date: 2024-06-23 09:46:49 -0400 (Sun, 23 Jun 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped


CHECK results for sesame on merida1

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.

raw results


Summary

Package: sesame
Version: 1.22.2
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_1.22.2.tar.gz
StartedAt: 2024-10-17 13:05:09 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 13:38:30 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 2001.3 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.22.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-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 ‘1.22.2’
* 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            174.643  7.950 216.705
imputeBetasByGenomicNeighbors  62.375  1.723  72.220
inferSex                       37.950  1.282  44.473
sesameQC_calcStats             35.614  2.320  43.745
KYCG_plotMeta                  34.077  1.186  40.852
compareMouseStrainReference    31.561  0.999  52.034
KYCG_plotEnrichAll             30.603  1.519  38.892
imputeBetas                    29.233  1.785  36.011
sesameQC_plotHeatSNPs          28.537  1.665  36.009
compareReference               28.823  0.821  35.857
KYCG_annoProbes                24.460  1.364  30.209
diffRefSet                     24.193  0.916  29.644
ELBAR                          22.275  2.689  29.139
matchDesign                    21.742  1.021  25.589
inferSpecies                   21.444  1.106  25.513
getRefSet                      19.568  0.680  22.944
sesameQC_plotBar               18.920  0.506  23.095
KYCG_plotMetaEnrichment        18.679  0.738  22.371
DML                            17.134  1.768  21.913
testEnrichmentSEA              16.992  1.144  22.081
sesameQC_plotBetaByDesign      16.130  1.547  21.137
sdf_read_table                 16.090  1.467  20.046
DMR                            16.508  0.469  20.102
KYCG_buildGeneDBs              16.247  0.722  20.071
visualizeGene                  15.776  0.616  19.863
inferStrain                    14.707  0.986  19.851
deidentify                     14.585  0.503  17.869
inferTissue                    11.593  1.743  15.208
reIdentify                     12.324  0.334  14.467
estimateLeukocyte              11.785  0.676  17.592
getMask                        11.291  0.726  14.459
openSesame                     10.322  1.194  13.309
dbStats                        10.356  0.802  13.386
KYCG_plotSetEnrichment          9.849  0.529  11.963
createUCSCtrack                 9.864  0.467  12.145
testEnrichment                  8.917  1.075  11.800
dyeBiasCorrMostBalanced         9.423  0.392  11.686
probeSuccessRate                8.799  0.801  11.314
updateSigDF                     8.657  0.635  11.628
dyeBiasNL                       8.165  0.510  10.256
sesameQC_rankStats              6.923  0.799   9.136
bisConversionControl            7.156  0.296   8.502
prepSesame                      6.802  0.527   9.010
noMasked                        5.869  0.339   7.290
scrubSoft                       5.138  0.957   6.944
sdf_write_table                 5.572  0.355   6.858
totalIntensities                5.145  0.399   7.137
summaryExtractTest              4.272  1.153   6.536
KYCG_plotWaterfall              5.124  0.250   6.215
print.DMLSummary                4.355  1.011   6.458
mapToMammal40                   4.861  0.477   6.116
detectionPnegEcdf               5.056  0.209   6.307
KYCG_getDBs                     4.871  0.374   6.633
parseGEOsignalMU                4.970  0.221   6.042
meanIntensity                   4.557  0.490   5.839
dyeBiasCorr                     4.639  0.317   5.973
checkLevels                     4.383  0.326   8.549
KYCG_plotPointRange             4.156  0.234   5.226
qualityMask                     3.812  0.545   5.087
* 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


Installation output

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)

Tests output

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, 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 
 36.189   3.520  46.119 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0000.0010.001
DML17.134 1.76821.913
DMLpredict2.4930.1793.194
DMR16.508 0.46920.102
ELBAR22.275 2.68929.139
KYCG_annoProbes24.460 1.36430.209
KYCG_buildGeneDBs16.247 0.72220.071
KYCG_getDBs4.8710.3746.633
KYCG_listDBGroups0.0580.0030.074
KYCG_loadDBs0.0000.0010.001
KYCG_plotBar0.4070.0290.521
KYCG_plotDot1.3020.0721.683
KYCG_plotEnrichAll30.603 1.51938.892
KYCG_plotLollipop0.3970.0120.481
KYCG_plotManhattan1.5480.2942.258
KYCG_plotMeta34.077 1.18640.852
KYCG_plotMetaEnrichment18.679 0.73822.371
KYCG_plotPointRange4.1560.2345.226
KYCG_plotSetEnrichment 9.849 0.52911.963
KYCG_plotVolcano0.3220.0030.345
KYCG_plotWaterfall5.1240.2506.215
MValueToBetaValue0.0010.0010.001
SigDF0.5650.0730.800
addMask0.1430.0000.160
aggregateTestEnrichments3.4320.1643.972
betasCollapseToPfx0.0290.0010.035
bisConversionControl7.1560.2968.502
calcEffectSize2.5790.1733.363
checkLevels4.3830.3268.549
cnSegmentation0.5590.0980.767
compareMouseStrainReference31.561 0.99952.034
compareMouseTissueReference0.0000.0000.001
compareReference28.823 0.82135.857
controls3.6420.3104.921
createUCSCtrack 9.864 0.46712.145
dataFrame2sesameQC2.0970.1952.759
dbStats10.356 0.80213.386
deidentify14.585 0.50317.869
detectionPnegEcdf5.0560.2096.307
diffRefSet24.193 0.91629.644
dmContrasts3.0700.2513.993
dyeBiasCorr4.6390.3175.973
dyeBiasCorrMostBalanced 9.423 0.39211.686
dyeBiasL3.8130.2024.795
dyeBiasNL 8.165 0.51010.256
estimateLeukocyte11.785 0.67617.592
formatVCF3.6680.3354.894
getAFTypeIbySumAlleles2.9840.2983.953
getAFs1.7410.1402.296
getBetas1.3840.1361.862
getMask11.291 0.72614.459
getRefSet19.568 0.68022.944
imputeBetas29.233 1.78536.011
imputeBetasByGenomicNeighbors62.375 1.72372.220
imputeBetasMatrixByMean0.0020.0010.004
inferEthnicity0.0010.0000.002
inferInfiniumIChannel0.8931.5502.770
inferSex37.950 1.28244.473
inferSpecies21.444 1.10625.513
inferStrain14.707 0.98619.851
inferTissue11.593 1.74315.208
initFileSet2.2820.3303.003
listAvailableMasks2.3090.2382.812
mLiftOver0.0010.0050.006
mapFileSet0.0610.0050.071
mapToMammal404.8610.4776.116
matchDesign21.742 1.02125.589
meanIntensity4.5570.4905.839
medianTotalIntensity1.3680.1201.666
noMasked5.8690.3397.290
noob3.3280.3164.143
openSesame10.322 1.19413.309
openSesameToFile3.1050.3613.897
pOOBAH2.2300.0152.445
palgen0.0690.0140.128
parseGEOsignalMU4.9700.2216.042
predictAge3.9300.1874.712
predictAgeHorvath3530.0000.0010.000
predictAgeSkinBlood0.0010.0010.001
predictMouseAgeInMonth0.0000.0000.001
prefixMask1.2000.0081.380
prefixMaskButC0.3490.0040.417
prefixMaskButCG0.1410.0040.175
prepSesame6.8020.5279.010
prepSesameList0.0030.0020.007
print.DMLSummary4.3551.0116.458
print.fileSet2.2040.3293.006
probeID_designType0.0000.0000.001
probeSuccessRate 8.799 0.80111.314
qualityMask3.8120.5455.087
reIdentify12.324 0.33414.467
readFileSet0.0910.0120.110
readIDATpair0.2390.0040.252
recommendedMaskNames0.0000.0000.001
resetMask0.7280.1171.161
scrub3.5750.0613.952
scrubSoft5.1380.9576.944
sdfPlatform0.5820.0860.825
sdf_read_table16.090 1.46720.046
sdf_write_table5.5720.3556.858
searchIDATprefixes0.0080.0050.017
sesame-package3.5750.2044.356
sesameAnno_attachManifest0.0000.0000.001
sesameAnno_buildAddressFile0.0000.0010.001
sesameAnno_buildManifestGRanges0.0010.0000.001
sesameAnno_download0.0000.0010.002
sesameAnno_readManifestTSV0.0000.0010.002
sesameQC_calcStats35.614 2.32043.745
sesameQC_getStats3.4310.0243.989
sesameQC_plotBar18.920 0.50623.095
sesameQC_plotBetaByDesign16.130 1.54721.137
sesameQC_plotHeatSNPs28.537 1.66536.009
sesameQC_plotIntensVsBetas2.8830.2583.581
sesameQC_plotRedGrnQQ2.3580.3493.094
sesameQC_rankStats6.9230.7999.136
sesame_checkVersion0.0060.0010.007
sesamize0.0000.0010.001
setMask0.1580.0020.168
signalMU1.3030.1011.675
sliceFileSet0.0600.0060.081
summaryExtractTest4.2721.1536.536
testEnrichment 8.917 1.07511.800
testEnrichmentGene174.643 7.950216.705
testEnrichmentSEA16.992 1.14422.081
totalIntensities5.1450.3997.137
updateSigDF 8.657 0.63511.628
visualizeGene15.776 0.61619.863
visualizeProbes3.4120.0544.044
visualizeRegion0.7730.0060.887
visualizeSegments2.3830.8293.894