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This page was generated on 2024-03-27 11:38:07 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 1934/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.20.0  (landing page)
Wanding Zhou
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_18
git_last_commit: a980995
git_last_commit_date: 2023-10-24 11:06:17 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

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: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2024-03-26 08:36:45 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 09:05:58 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 1753.5 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/sesame.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.20.0’
* 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 R 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 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          175.584  7.063 202.861
sesameQC_calcStats           36.198  1.715  38.584
KYCG_plotMeta                31.679  1.148  34.791
sesameQC_plotHeatSNPs        29.858  1.789  32.851
KYCG_plotEnrichAll           29.298  1.327  33.564
compareMouseStrainReference  29.187  0.574  32.156
compareReference             26.708  0.864  30.145
inferSpecies                 24.557  1.002  28.703
ELBAR                        21.638  2.889  26.531
matchDesign                  23.327  0.768  25.604
diffRefSet                   21.465  0.861  24.327
KYCG_annoProbes              21.354  0.962  23.640
convertTo                    20.615  0.607  23.651
sesameQC_plotBar             19.484  0.681  21.317
getRefSet                    19.236  0.683  21.924
testEnrichmentSEA            18.278  0.959  21.112
DML                          16.186  1.904  20.271
inferTissue                  16.263  1.436  19.823
sesameQC_plotBetaByDesign    16.140  1.260  17.464
KYCG_buildGeneDBs            16.796  0.570  18.395
KYCG_plotMetaEnrichment      16.645  0.696  18.541
sdf_read_table               16.165  0.614  18.141
visualizeGene                15.999  0.548  18.947
DMR                          15.622  0.641  20.372
getSexInfo                   14.653  0.583  17.504
deidentify                   13.666  0.468  15.080
inferStrain                  13.048  0.847  17.570
createUCSCtrack              11.366  0.432  14.693
dbStats                      10.940  0.755  13.299
reIdentify                   11.469  0.226  12.294
estimateLeukocyte            10.581  0.603  13.132
KYCG_plotSetEnrichment       10.260  0.598  11.535
dyeBiasCorrMostBalanced      10.027  0.343  11.388
openSesame                    9.050  0.787  10.948
dyeBiasNL                     9.161  0.496  11.186
testEnrichment                8.582  0.803  11.024
probeSuccessRate              8.722  0.460  14.126
inferSex                      8.421  0.475   9.760
getMask                       8.010  0.472  10.241
bisConversionControl          7.287  0.289   8.463
prepSesame                    6.416  0.494   8.443
visualizeProbes               6.649  0.179   7.493
sdf_write_table               6.175  0.303   7.055
scrubSoft                     5.210  0.796   6.239
parseGEOsignalMU              5.099  0.531   6.575
sesameQC_rankStats            5.185  0.371   6.213
totalIntensities              5.058  0.405   6.309
KYCG_plotWaterfall            5.165  0.286   5.849
inferSexKaryotypes            5.150  0.248   5.654
meanIntensity                 4.700  0.638   5.984
updateSigDF                   5.007  0.315   6.440
mapToMammal40                 4.686  0.438   5.969
summaryExtractTest            4.188  0.815   6.230
detectionPnegEcdf             4.749  0.199   5.731
KYCG_getDBs                   4.553  0.360   5.521
checkLevels                   4.432  0.454   5.161
dyeBiasCorr                   4.562  0.292   5.573
print.DMLSummary              4.102  0.735   5.981
qualityMask                   4.259  0.506   6.074
predictAge                    3.806  0.165   5.490
formatVCF                     3.575  0.312   7.129
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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, sort, 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 1 ]
> 
> proc.time()
   user  system elapsed 
 35.190   2.743  42.014 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0000.0000.001
DML16.186 1.90420.271
DMLpredict2.3750.1982.981
DMR15.622 0.64120.372
ELBAR21.638 2.88926.531
KYCG_annoProbes21.354 0.96223.640
KYCG_buildGeneDBs16.796 0.57018.395
KYCG_getDBs4.5530.3605.521
KYCG_listDBGroups0.0550.0040.064
KYCG_loadDBs0.0000.0010.002
KYCG_plotBar0.4050.0490.493
KYCG_plotDot1.4720.1541.773
KYCG_plotEnrichAll29.298 1.32733.564
KYCG_plotLollipop0.3710.0240.424
KYCG_plotManhattan1.3710.1501.636
KYCG_plotMeta31.679 1.14834.791
KYCG_plotMetaEnrichment16.645 0.69618.541
KYCG_plotPointRange4.2800.2444.763
KYCG_plotSetEnrichment10.260 0.59811.535
KYCG_plotVolcano0.3010.0060.319
KYCG_plotWaterfall5.1650.2865.849
MValueToBetaValue0.0000.0010.001
SigDF0.5210.0730.681
addMask0.1310.0010.133
aggregateTestEnrichments4.2430.0704.415
betasCollapseToPfx0.0040.0010.006
bisConversionControl7.2870.2898.463
calcEffectSize2.3980.2092.765
checkLevels4.4320.4545.161
cnSegmentation0.5530.1010.760
compareMouseStrainReference29.187 0.57432.156
compareMouseTissueReference0.0000.0010.001
compareReference26.708 0.86430.145
controls3.5770.2924.599
convertTo20.615 0.60723.651
createUCSCtrack11.366 0.43214.693
dataFrame2sesameQC2.1580.2142.746
dbStats10.940 0.75513.299
deidentify13.666 0.46815.080
detectionPnegEcdf4.7490.1995.731
diffRefSet21.465 0.86124.327
dmContrasts2.9710.2123.548
dyeBiasCorr4.5620.2925.573
dyeBiasCorrMostBalanced10.027 0.34311.388
dyeBiasL3.0870.1584.998
dyeBiasNL 9.161 0.49611.186
estimateLeukocyte10.581 0.60313.132
formatVCF3.5750.3127.129
getAFTypeIbySumAlleles2.9230.2574.597
getAFs1.7890.1172.698
getBetas1.4230.1323.294
getMask 8.010 0.47210.241
getRefSet19.236 0.68321.924
getSexInfo14.653 0.58317.504
imputeTo2.8820.2193.891
inferEthnicity4.0420.2734.747
inferInfiniumIChannel0.9141.4632.520
inferSex8.4210.4759.760
inferSexKaryotypes5.1500.2485.654
inferSpecies24.557 1.00228.703
inferStrain13.048 0.84717.570
inferTissue16.263 1.43619.823
initFileSet2.0840.2842.834
listAvailableMasks2.9050.1883.473
mapFileSet0.0590.0050.065
mapToMammal404.6860.4385.969
matchDesign23.327 0.76825.604
meanIntensity4.7000.6385.984
medianTotalIntensity1.4320.1002.231
noMasked3.0760.0933.887
noob3.5510.5394.257
openSesame 9.050 0.78710.948
openSesameToFile2.6560.0252.780
pOOBAH2.3550.0172.613
palgen0.0690.0110.082
parseGEOsignalMU5.0990.5316.575
predictAge3.8060.1655.490
predictAgeHorvath3530.0010.0000.000
predictAgeSkinBlood0.0010.0000.001
predictMouseAgeInMonth0.0000.0010.001
prefixMask1.1410.0041.158
prefixMaskButC0.3150.0020.320
prefixMaskButCG0.1260.0010.129
prepSesame6.4160.4948.443
prepSesameList0.0040.0020.005
print.DMLSummary4.1020.7355.981
print.fileSet2.0710.2332.674
probeID_designType0.0000.0010.001
probeSuccessRate 8.722 0.46014.126
qualityMask4.2590.5066.074
reIdentify11.469 0.22612.294
readFileSet0.0940.0060.107
readIDATpair0.2270.0040.237
recommendedMaskNames0.0000.0010.002
resetMask0.6910.0831.046
scrub3.7560.3394.266
scrubSoft5.2100.7966.239
sdfPlatform0.5470.0900.942
sdf_read_table16.165 0.61418.141
sdf_write_table6.1750.3037.055
searchIDATprefixes0.0070.0050.013
sesame-package3.8450.3974.400
sesameAnno_buildAddressFile0.0010.0000.001
sesameAnno_buildManifestGRanges0.0000.0010.001
sesameAnno_download0.0000.0010.001
sesameAnno_get0.0010.0010.001
sesameAnno_readManifestTSV0.0000.0010.001
sesameData_getAnno000
sesameQC_calcStats36.198 1.71538.584
sesameQC_getStats3.4450.0183.502
sesameQC_plotBar19.484 0.68121.317
sesameQC_plotBetaByDesign16.140 1.26017.464
sesameQC_plotHeatSNPs29.858 1.78932.851
sesameQC_plotIntensVsBetas2.9200.3543.877
sesameQC_plotRedGrnQQ2.2470.3962.948
sesameQC_rankStats5.1850.3716.213
sesame_checkVersion0.0060.0010.008
sesamize0.0000.0000.001
setMask0.1590.0020.168
signalMU1.5410.1882.200
sliceFileSet0.0610.0050.068
summaryExtractTest4.1880.8156.230
testEnrichment 8.582 0.80311.024
testEnrichmentGene175.584 7.063202.861
testEnrichmentSEA18.278 0.95921.112
totalIntensities5.0580.4056.309
updateSigDF5.0070.3156.440
visualizeGene15.999 0.54818.947
visualizeProbes6.6490.1797.493
visualizeRegion1.1530.0201.190
visualizeSegments2.5480.8944.090