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This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4505
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4486
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1938/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.24.0  (landing page)
Wanding Zhou
Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_20
git_last_commit: e86f791
git_last_commit_date: 2024-10-29 10:29:34 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for sesame on kjohnson3

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: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2024-11-09 13:14:07 -0500 (Sat, 09 Nov 2024)
EndedAt: 2024-11-09 13:22:47 -0500 (Sat, 09 Nov 2024)
EllapsedTime: 520.1 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.24.0.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: 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 13.6.7
* 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 ...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            14.101  0.685  14.798
imputeBetasByGenomicNeighbors 12.199  0.438  12.640
inferSex                       8.047  0.400   8.447
sesameQC_calcStats             7.716  0.639   8.357
KYCG_plotMeta                  6.800  0.240   7.041
sesameQC_plotHeatSNPs          6.159  0.573   6.733
imputeBetas                    5.829  0.336   6.168
KYCG_plotEnrichAll             5.798  0.284   6.088
sesameQC_plotBar               5.729  0.145   5.878
ELBAR                          4.646  0.802   5.452
inferSpecies                   5.051  0.192   5.248
* 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-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)

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: 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':

    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 
  7.093   0.379   7.498 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML2.4850.2262.713
DMLpredict0.3340.0250.359
DMR2.1450.0562.201
ELBAR4.6460.8025.452
KYCG_annoProbes4.6300.1664.797
KYCG_buildGeneDBs4.3230.0964.419
KYCG_getDBs0.7830.0430.826
KYCG_listDBGroups0.1050.0010.106
KYCG_loadDBs0.0000.0000.001
KYCG_plotBar0.0570.0010.057
KYCG_plotDot0.0810.0000.081
KYCG_plotEnrichAll5.7980.2846.088
KYCG_plotLollipop0.0460.0020.048
KYCG_plotManhattan0.6260.0290.654
KYCG_plotMeta6.8000.2407.041
KYCG_plotMetaEnrichment3.7290.1293.858
KYCG_plotPointRange0.5910.0920.684
KYCG_plotSetEnrichment1.7950.1801.975
KYCG_plotVolcano0.0430.0050.048
KYCG_plotWaterfall0.6810.0810.763
MValueToBetaValue0.0010.0000.000
SigDF0.0720.0090.082
addMask0.0150.0010.015
aggregateTestEnrichments0.5180.0700.589
betasCollapseToPfx0.0040.0000.004
bisConversionControl2.1540.0502.203
calcEffectSize0.3450.0260.371
checkLevels1.1290.0751.206
cnSegmentation0.0740.0160.092
compareMouseStrainReference3.4480.1703.621
compareMouseTissueReference000
compareReference3.5660.1443.712
controls0.5840.0620.645
createUCSCtrack1.7130.1461.859
dbStats1.8310.1571.992
deidentify1.6760.1281.808
detectionPnegEcdf0.9030.0360.939
diffRefSet4.6670.2964.966
dmContrasts0.5840.0430.627
dyeBiasCorr0.7920.0610.852
dyeBiasCorrMostBalanced2.7330.0542.787
dyeBiasL0.8990.0220.921
dyeBiasNL2.1580.2022.359
estimateLeukocyte2.2200.0942.315
formatVCF0.6540.0410.696
getAFTypeIbySumAlleles0.4820.0690.553
getAFs0.3360.0330.368
getBetas0.2410.0220.263
getMask1.9430.1672.113
getRefSet4.2840.1434.428
imputeBetas5.8290.3366.168
imputeBetasByGenomicNeighbors12.199 0.43812.640
imputeBetasMatrixByMean0.0010.0000.000
inferEthnicity000
inferInfiniumIChannel0.1320.1330.267
inferSex8.0470.4008.447
inferSpecies5.0510.1925.248
inferStrain2.4300.1922.622
inferTissue2.1460.2502.396
initFileSet0.3290.0340.365
listAvailableMasks0.3630.0530.417
mLiftOver0.0000.0010.000
mapFileSet0.0160.0010.017
mapToMammal400.7490.0970.848
matchDesign4.3850.2434.630
meanIntensity0.8380.0500.888
medianTotalIntensity0.2580.0420.299
noMasked1.2620.1091.370
noob0.7830.1290.912
openSesame1.6320.1551.791
openSesameToFile0.5240.0350.558
pOOBAH0.4900.0140.505
palgen0.0150.0020.017
parseGEOsignalMU1.2090.0731.281
predictAge0.8790.0270.907
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.2340.0010.236
prefixMaskButC0.0630.0010.064
prefixMaskButCG0.0250.0000.026
prepSesame1.2350.1401.374
prepSesameList000
print.DMLSummary1.1100.1521.261
print.fileSet0.3320.0390.371
probeID_designType000
probeSuccessRate1.6840.1101.795
qualityMask0.6050.0720.678
reIdentify1.3150.0491.365
readFileSet0.0270.0020.028
readIDATpair0.0480.0020.051
recommendedMaskNames000
resetMask0.1120.0110.124
scrub0.8140.0710.885
scrubSoft1.2220.2611.484
sdfPlatform0.0650.0090.074
sdf_read_table3.0550.1373.194
sdf_write_table0.8910.0280.920
searchIDATprefixes0.0020.0010.002
sesame-package0.5660.0330.599
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats7.7160.6398.357
sesameQC_getStats0.8260.0190.846
sesameQC_plotBar5.7290.1455.878
sesameQC_plotBetaByDesign3.8610.4644.325
sesameQC_plotHeatSNPs6.1590.5736.733
sesameQC_plotIntensVsBetas0.6230.0720.707
sesameQC_plotRedGrnQQ0.5130.0550.570
sesameQC_rankStats1.0430.2211.266
sesameQCtoDF0.7870.0640.850
sesame_checkVersion0.0010.0000.001
sesamize000
setMask0.0190.0040.023
signalMU0.2000.0430.243
sliceFileSet0.0140.0010.015
summaryExtractTest0.9130.0770.991
testEnrichment1.4110.1711.583
testEnrichmentGene14.101 0.68514.798
testEnrichmentSEA4.2870.2264.514
totalIntensities0.9670.0701.038
updateSigDF0.8510.1060.957
visualizeGene3.6820.1353.819
visualizeProbes0.2740.0050.278
visualizeRegion0.2120.0060.218
visualizeSegments0.9910.0761.067