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This page was generated on 2024-05-04 11:37:11 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1.22.0  (landing page)
Wanding Zhou
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_19
git_last_commit: 5afa15d
git_last_commit_date: 2024-04-30 11:07:28 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for sesame on nebbiolo1


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: 1.22.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings sesame_1.22.0.tar.gz
StartedAt: 2024-05-04 03:38:01 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 03:59:05 -0400 (Sat, 04 May 2024)
EllapsedTime: 1263.1 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings sesame_1.22.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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          102.198  3.463 108.938
inferSex                     34.175  1.873  36.681
KYCG_plotMeta                23.445  1.320  25.240
KYCG_plotEnrichAll           20.582  2.427  24.122
ELBAR                        18.476  0.716  19.351
sesameQC_calcStats           18.727  0.204  19.086
sesameQC_plotHeatSNPs        17.835  0.252  18.247
KYCG_annoProbes              15.593  1.540  17.657
inferSpecies                 15.419  1.092  17.001
KYCG_plotMetaEnrichment      13.867  1.511  15.994
getRefSet                    12.067  2.435  14.819
diffRefSet                   12.900  1.059  14.278
compareReference             12.419  1.320  14.060
compareMouseStrainReference  12.339  1.032  13.688
KYCG_buildGeneDBs            11.772  1.167  13.255
visualizeGene                12.537  0.396  13.418
sesameQC_plotBar             12.359  0.304  12.977
matchDesign                  10.585  0.268  11.017
testEnrichmentSEA             9.551  0.376  10.436
estimateLeukocyte             8.756  1.056  10.125
DMR                           8.921  0.703   9.984
sesameQC_plotBetaByDesign     9.284  0.188   9.473
dbStats                       7.563  0.951   8.837
sdf_read_table                8.233  0.172   8.723
DML                           7.143  0.804   8.334
inferStrain                   7.034  0.517   7.864
dyeBiasCorrMostBalanced       6.569  0.468   7.352
KYCG_plotSetEnrichment        6.305  0.639   7.262
createUCSCtrack               6.177  0.593   7.096
dyeBiasNL                     6.295  0.432   6.925
inferTissue                   6.216  0.260   6.790
deidentify                    5.915  0.492   6.729
bisConversionControl          5.631  0.464   6.411
getMask                       5.525  0.507   6.551
testEnrichment                5.569  0.288   6.331
probeSuccessRate              5.370  0.236   6.085
openSesame                    4.958  0.300   5.576
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

sesame.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 18.232   1.089  19.624 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0010.0000.000
DML7.1430.8048.334
DMLpredict1.4890.2041.848
DMR8.9210.7039.984
ELBAR18.476 0.71619.351
KYCG_annoProbes15.593 1.54017.657
KYCG_buildGeneDBs11.772 1.16713.255
KYCG_getDBs3.2280.3243.872
KYCG_listDBGroups0.0340.0040.038
KYCG_loadDBs000
KYCG_plotBar0.2040.0280.232
KYCG_plotDot0.6530.1240.776
KYCG_plotEnrichAll20.582 2.42724.122
KYCG_plotLollipop0.1640.0160.180
KYCG_plotManhattan1.7780.2522.030
KYCG_plotMeta23.445 1.32025.240
KYCG_plotMetaEnrichment13.867 1.51115.994
KYCG_plotPointRange3.0760.2283.503
KYCG_plotSetEnrichment6.3050.6397.262
KYCG_plotVolcano0.1400.0170.157
KYCG_plotWaterfall2.9000.3483.412
MValueToBetaValue000
SigDF0.4220.0690.650
addMask0.1000.0200.119
aggregateTestEnrichments2.7420.3083.050
betasCollapseToPfx0.0160.0080.025
bisConversionControl5.6310.4646.411
calcEffectSize1.5490.1561.862
checkLevels4.2900.5044.994
cnSegmentation0.4210.0360.613
compareMouseStrainReference12.339 1.03213.688
compareMouseTissueReference0.0000.0000.001
compareReference12.419 1.32014.060
controls2.3940.2792.988
createUCSCtrack6.1770.5937.096
dataFrame2sesameQC1.2650.1251.558
dbStats7.5630.9518.837
deidentify5.9150.4926.729
detectionPnegEcdf3.0640.2953.516
diffRefSet12.900 1.05914.278
dmContrasts2.4780.2472.882
dyeBiasCorr3.1750.3413.844
dyeBiasCorrMostBalanced6.5690.4687.352
dyeBiasL3.7550.7084.662
dyeBiasNL6.2950.4326.925
estimateLeukocyte 8.756 1.05610.125
formatVCF2.5600.3203.195
getAFTypeIbySumAlleles2.1290.2962.738
getAFs1.2950.2031.655
getBetas0.9420.1921.292
getMask5.5250.5076.551
getRefSet12.067 2.43514.819
imputeBetasMatrixByMean0.0050.0000.005
inferEthnicity1.9240.1482.230
inferInfiniumIChannel0.2820.6240.906
inferSex34.175 1.87336.681
inferSpecies15.419 1.09217.001
inferStrain7.0340.5177.864
inferTissue6.2160.2606.790
initFileSet1.3050.0761.565
listAvailableMasks1.8040.0522.012
mLiftOver0.0010.0000.001
mapFileSet0.0330.0000.033
mapToMammal402.9160.1553.427
matchDesign10.585 0.26811.017
meanIntensity2.9290.1643.410
medianTotalIntensity0.8680.0761.101
noMasked1.7120.1191.990
noob2.0610.0442.105
openSesame4.9580.3005.576
openSesameToFile1.3530.0281.381
pOOBAH1.210.021.23
palgen0.0340.0040.038
parseGEOsignalMU3.3340.1243.616
predictAge2.2680.0672.495
predictAgeHorvath353000
predictAgeSkinBlood0.0000.0010.000
predictMouseAgeInMonth0.0000.0000.001
prefixMask0.4140.0020.417
prefixMaskButC0.1040.0040.108
prefixMaskButCG0.0370.0000.036
prepSesame3.3500.1643.671
prepSesameList0.0010.0000.001
print.DMLSummary3.2750.2083.797
print.fileSet1.3020.0641.523
probeID_designType0.0000.0000.001
probeSuccessRate5.3700.2366.085
qualityMask2.6980.1363.161
reIdentify4.2580.1524.567
readFileSet0.0510.0040.055
readIDATpair0.1310.0000.131
recommendedMaskNames0.0000.0000.001
resetMask0.4570.0520.666
scrub2.2470.1202.367
scrubSoft3.1210.0363.157
sdfPlatform0.4410.0800.678
sdf_read_table8.2330.1728.723
sdf_write_table2.6600.1032.997
searchIDATprefixes0.0050.0000.005
sesame-package2.5510.1602.870
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download0.0000.0010.001
sesameAnno_get000
sesameAnno_readManifestTSV000
sesameData_getAnno000
sesameQC_calcStats18.727 0.20419.086
sesameQC_getStats1.7570.0241.781
sesameQC_plotBar12.359 0.30412.977
sesameQC_plotBetaByDesign9.2840.1889.473
sesameQC_plotHeatSNPs17.835 0.25218.247
sesameQC_plotIntensVsBetas1.8020.0682.026
sesameQC_plotRedGrnQQ1.8820.0522.105
sesameQC_rankStats3.3480.1393.816
sesame_checkVersion0.0030.0000.003
sesamize000
setMask0.0840.0010.084
signalMU0.7470.0440.951
sliceFileSet0.0330.0000.033
summaryExtractTest2.5930.1203.038
testEnrichment5.5690.2886.331
testEnrichmentGene102.198 3.463108.938
testEnrichmentSEA 9.551 0.37610.436
totalIntensities2.9990.1483.518
updateSigDF3.1790.1683.663
visualizeGene12.537 0.39613.418
visualizeProbes0.9860.0120.998
visualizeRegion0.5670.0000.568
visualizeSegments2.1570.0522.367