Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:52 -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 palomino4


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: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sesame.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings sesame_1.16.1.tar.gz
StartedAt: 2023-04-11 05:57:46 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 06:11:57 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 850.9 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sesame.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings sesame_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/sesame.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'sesame/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sesame' version '1.16.1'
* 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 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 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          30.25   1.45   32.97
sesameQC_plotHeatSNPs       24.47   0.89   25.50
sesameQC_calcStats          23.13   0.80   23.97
matchDesign                 18.39   0.67   19.10
inferSpecies                15.63   0.63   16.79
DMR                         15.65   0.48   16.82
KYCG_plotMeta               14.85   0.65   15.92
sdf_read_table              14.00   0.35   14.41
KYCG_annoProbes             13.30   0.58   14.16
sesameQC_plotBar            13.25   0.39   14.57
sesameQC_plotBetaByDesign   12.08   0.76   12.85
KYCG_plotMetaEnrichment     11.54   0.68   12.30
diffRefSet                  11.22   0.49   12.50
compareMouseStrainReference 11.21   0.47   11.89
KYCG_buildGeneDBs           11.31   0.28   12.09
compareReference            10.94   0.59   11.56
inferTissue                 10.52   0.72   11.28
DML                          8.32   1.96   10.34
testEnrichmentSEA            9.46   0.65   10.17
testEnrichment               9.26   0.56    9.94
getRefSet                    9.26   0.38    9.67
detectionIB                  8.31   0.72    9.06
visualizeGene                8.32   0.44    8.82
inferStrain                  7.59   0.71    8.35
getSexInfo                   7.75   0.44    8.27
estimateLeukocyte            7.39   0.41    8.29
sdf_write_table              7.19   0.21    7.43
dbStats                      6.42   0.58    7.68
dyeBiasNL                    6.25   0.42    6.67
createUCSCtrack              6.00   0.24    6.52
dyeBiasCorrMostBalanced      5.75   0.31    6.86
probeSuccessRate             5.64   0.39    6.09
KYCG_plotSetEnrichment       5.56   0.40    6.05
deidentify                   4.79   0.26    5.28
reIdentify                   4.78   0.13    5.03
* 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

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  21.68    3.00   48.65 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML 8.32 1.9610.34
DMLpredict1.240.111.36
DMR15.65 0.4816.82
KYCG_annoProbes13.30 0.5814.16
KYCG_buildGeneDBs11.31 0.2812.09
KYCG_getDBs3.110.203.47
KYCG_listDBGroups0.050.000.05
KYCG_loadDBs000
KYCG_plotBar0.330.050.38
KYCG_plotDot0.230.000.23
KYCG_plotEnrichAll30.25 1.4532.97
KYCG_plotLollipop0.160.000.15
KYCG_plotManhattan1.650.141.80
KYCG_plotMeta14.85 0.6515.92
KYCG_plotMetaEnrichment11.54 0.6812.30
KYCG_plotPointRange3.300.133.56
KYCG_plotSetEnrichment5.560.406.05
KYCG_plotVolcano0.140.020.16
KYCG_plotWaterfall2.640.222.89
MValueToBetaValue000
SigDF0.250.030.30
addMask0.060.000.07
aggregateTestEnrichments1.990.082.06
bisConversionControl4.220.204.97
calcEffectSize0.960.241.22
checkLevels3.820.204.26
cnSegmentation0.220.060.41
compareMouseStrainReference11.21 0.4711.89
compareMouseTissueReference000
compareReference10.94 0.5911.56
controls1.920.192.14
createUCSCtrack6.000.246.52
dataFrame2sesameQC0.960.101.20
dbStats6.420.587.68
deidentify4.790.265.28
detectionIB8.310.729.06
detectionPnegEcdf1.220.001.22
diffRefSet11.22 0.4912.50
dmContrasts1.840.111.97
dyeBiasCorr2.450.142.64
dyeBiasCorrMostBalanced5.750.316.86
dyeBiasL2.520.062.60
dyeBiasNL6.250.426.67
estimateLeukocyte7.390.418.29
formatVCF3.170.233.46
getAFTypeIbySumAlleles1.390.191.65
getAFs0.970.101.08
getBetas0.830.071.05
getRefSet9.260.389.67
getSexInfo7.750.448.27
inferEthnicity3.180.183.50
inferInfiniumIChannel0.430.330.76
inferSex4.160.384.56
inferSexKaryotypes2.810.092.93
inferSpecies15.63 0.6316.79
inferStrain7.590.718.35
inferTissue10.52 0.7211.28
initFileSet1.290.111.44
listAvailableMasks1.780.142.01
mapFileSet0.030.000.04
mapToMammal403.190.243.47
matchDesign18.39 0.6719.10
meanIntensity2.480.232.75
medianTotalIntensity0.780.100.89
noMasked2.340.172.66
noob2.630.192.81
openSesame3.690.424.36
openSesameToFile1.810.181.98
pOOBAH1.530.011.55
palgen0.060.020.08
parseGEOsignalMU2.880.173.07
predictAge2.400.142.58
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.460.000.45
prefixMaskButC0.150.020.18
prefixMaskButCG0.050.000.04
prepSesame4.380.284.68
prepSesameList000
print.DMLSummary2.770.363.17
print.fileSet1.110.111.25
probeID_designType000
probeSuccessRate5.640.396.09
qualityMask0.820.090.94
reIdentify4.780.135.03
readFileSet0.040.000.05
readIDATpair0.160.000.15
resetMask0.500.040.57
scrub2.890.193.07
scrubSoft4.160.274.43
sdfPlatform0.260.040.45
sdf_read_table14.00 0.3514.41
sdf_write_table7.190.217.43
searchIDATprefixes0.000.020.02
sesame-package1.910.172.22
sesameAnno_download000
sesameAnno_get000
sesameData_getAnno000
sesameQC_calcStats23.13 0.8023.97
sesameQC_getStats2.620.082.71
sesameQC_plotBar13.25 0.3914.57
sesameQC_plotBetaByDesign12.08 0.7612.85
sesameQC_plotHeatSNPs24.47 0.8925.50
sesameQC_plotIntensVsBetas2.140.182.45
sesameQC_plotRedGrnQQ1.260.121.53
sesameQC_rankStats3.360.283.83
setMask0.100.000.09
signalMU0.890.141.05
sliceFileSet0.040.000.04
summaryExtractTest2.450.212.72
testEnrichment9.260.569.94
testEnrichmentSEA 9.46 0.6510.17
totalIntensities2.700.242.97
updateSigDF3.270.363.80
visualizeGene8.320.448.82
visualizeProbes4.070.114.30
visualizeRegion0.290.000.30
visualizeSegments2.820.093.06