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This page was generated on 2023-04-12 11:05:19 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for sesame on nebbiolo2


To the developers/maintainers of the sesame package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1853/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.16.1  (landing page)
Wanding Zhou
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_16
git_last_commit: 6a20764
git_last_commit_date: 2022-11-13 15:36:35 -0400 (Sun, 13 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 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
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: sesame
Version: 1.16.1
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings sesame_1.16.1.tar.gz
StartedAt: 2023-04-10 23:58:36 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-11 00:17:24 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 1128.2 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings sesame_1.16.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/sesame.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.16.1’
* 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 loading without being on the library search path ... 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
KYCG_plotEnrichAll          31.667  0.684  34.091
sesameQC_calcStats          23.017  0.168  23.440
sesameQC_plotHeatSNPs       21.677  0.260  22.193
KYCG_plotMeta               20.634  0.232  21.556
inferSpecies                17.031  0.800  18.421
DMR                         16.724  0.376  17.781
diffRefSet                  14.199  0.288  14.851
sesameQC_plotBetaByDesign   13.780  0.280  14.061
matchDesign                 13.528  0.352  14.048
compareMouseStrainReference 13.032  0.176  13.648
KYCG_annoProbes             12.709  0.400  13.704
KYCG_plotMetaEnrichment     12.732  0.204  13.572
sesameQC_plotBar            12.047  0.236  12.796
compareReference            11.787  0.272  12.479
KYCG_buildGeneDBs           11.358  0.355  12.224
testEnrichment              11.068  0.296  12.396
getRefSet                   10.710  0.152  11.289
testEnrichmentSEA           10.576  0.180  11.450
sdf_read_table              10.174  0.140  10.651
inferTissue                 10.013  0.208  10.815
detectionIB                  9.814  0.156  10.140
visualizeGene                9.529  0.268  10.392
getSexInfo                   9.547  0.172  10.414
dbStats                      8.611  0.304   9.423
DML                          7.925  0.408   8.762
inferStrain                  7.582  0.356   8.445
createUCSCtrack              7.505  0.200   8.123
estimateLeukocyte            7.164  0.144   7.833
dyeBiasNL                    6.717  0.140   7.110
dyeBiasCorrMostBalanced      6.045  0.104   6.678
probeSuccessRate             5.983  0.132   6.895
deidentify                   6.043  0.056   6.609
KYCG_plotSetEnrichment       5.836  0.088   6.460
openSesame                   5.338  0.152   5.998
reIdentify                   5.052  0.040   5.349
bisConversionControl         4.973  0.088   5.480
updateSigDF                  4.642  0.152   5.216
* 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 ...
  ‘KYCG.Rmd’ using ‘UTF-8’... OK
  ‘QC.Rmd’ using ‘UTF-8’... OK
  ‘inferences.Rmd’ using ‘UTF-8’... OK
  ‘modeling.Rmd’ using ‘UTF-8’... OK
  ‘nonhuman.Rmd’ using ‘UTF-8’... OK
  ‘sesame.Rmd’ using ‘UTF-8’... OK
 NONE
* 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-3.16-bioc/R/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 21.483   0.963  22.850 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0010.0000.000
DML7.9250.4088.762
DMLpredict1.6240.0651.940
DMR16.724 0.37617.781
KYCG_annoProbes12.709 0.40013.704
KYCG_buildGeneDBs11.358 0.35512.224
KYCG_getDBs3.2840.0803.881
KYCG_listDBGroups0.0310.0000.031
KYCG_loadDBs0.0000.0000.001
KYCG_plotBar0.3500.0080.358
KYCG_plotDot0.2430.0080.251
KYCG_plotEnrichAll31.667 0.68434.091
KYCG_plotLollipop0.1490.0000.148
KYCG_plotManhattan1.4230.0041.427
KYCG_plotMeta20.634 0.23221.556
KYCG_plotMetaEnrichment12.732 0.20413.572
KYCG_plotPointRange4.0610.0884.406
KYCG_plotSetEnrichment5.8360.0886.460
KYCG_plotVolcano0.1540.0120.166
KYCG_plotWaterfall3.4160.0723.656
MValueToBetaValue000
SigDF0.4050.0160.680
addMask0.170.000.17
aggregateTestEnrichments2.4280.0322.460
bisConversionControl4.9730.0885.480
calcEffectSize1.4360.0201.728
checkLevels4.6080.1244.987
cnSegmentation0.4450.0160.630
compareMouseStrainReference13.032 0.17613.648
compareMouseTissueReference000
compareReference11.787 0.27212.479
controls2.2060.0762.616
createUCSCtrack7.5050.2008.123
dataFrame2sesameQC1.1930.0721.519
dbStats8.6110.3049.423
deidentify6.0430.0566.609
detectionIB 9.814 0.15610.140
detectionPnegEcdf1.1380.0161.154
diffRefSet14.199 0.28814.851
dmContrasts2.4650.1042.840
dyeBiasCorr3.6240.1204.255
dyeBiasCorrMostBalanced6.0450.1046.678
dyeBiasL3.2660.0883.611
dyeBiasNL6.7170.1407.110
estimateLeukocyte7.1640.1447.833
formatVCF3.4110.0763.993
getAFTypeIbySumAlleles1.6180.0642.191
getAFs1.1240.0201.312
getBetas0.9850.0321.272
getRefSet10.710 0.15211.289
getSexInfo 9.547 0.17210.414
inferEthnicity2.4770.0562.785
inferInfiniumIChannel0.4280.1200.548
inferSex4.2780.0444.746
inferSexKaryotypes3.1390.0323.442
inferSpecies17.031 0.80018.421
inferStrain7.5820.3568.445
inferTissue10.013 0.20810.815
initFileSet1.3100.0441.609
listAvailableMasks1.7830.0202.057
mapFileSet0.0330.0000.033
mapToMammal403.3410.0723.838
matchDesign13.528 0.35214.048
meanIntensity2.8330.0563.309
medianTotalIntensity0.9560.0841.293
noMasked1.6500.1601.978
noob2.1920.0922.284
openSesame5.3380.1525.998
openSesameToFile1.4040.0041.408
pOOBAH1.2910.0161.307
palgen0.0430.0000.044
parseGEOsignalMU3.4830.0603.711
predictAge2.7170.0922.976
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.4550.0040.459
prefixMaskButC0.1430.0000.144
prefixMaskButCG0.0450.0000.046
prepSesame4.2940.0884.594
prepSesameList0.0020.0000.002
print.DMLSummary4.0670.1524.642
print.fileSet1.4420.0361.646
probeID_designType0.0000.0000.001
probeSuccessRate5.9830.1326.895
qualityMask1.4390.0201.714
reIdentify5.0520.0405.349
readFileSet0.0500.0000.051
readIDATpair0.1180.0000.118
resetMask0.4250.0160.712
scrub2.4900.0442.534
scrubSoft3.8390.0563.895
sdfPlatform0.3710.0200.559
sdf_read_table10.174 0.14010.651
sdf_write_table2.5830.0562.991
searchIDATprefixes0.0080.0000.008
sesame-package1.9830.0402.281
sesameAnno_download000
sesameAnno_get0.0010.0000.000
sesameData_getAnno000
sesameQC_calcStats23.017 0.16823.440
sesameQC_getStats1.5180.0001.519
sesameQC_plotBar12.047 0.23612.796
sesameQC_plotBetaByDesign13.780 0.28014.061
sesameQC_plotHeatSNPs21.677 0.26022.193
sesameQC_plotIntensVsBetas2.5450.0402.754
sesameQC_plotRedGrnQQ2.1880.0082.366
sesameQC_rankStats3.7300.0924.349
setMask0.1060.0000.106
signalMU0.9180.0281.107
sliceFileSet0.0330.0000.034
summaryExtractTest2.4410.0802.943
testEnrichment11.068 0.29612.396
testEnrichmentSEA10.576 0.18011.450
totalIntensities2.9920.0803.495
updateSigDF4.6420.1525.216
visualizeGene 9.529 0.26810.392
visualizeProbes4.3460.0564.656
visualizeRegion0.5960.0040.600
visualizeSegments2.3450.0402.550