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This page was generated on 2022-07-01 12:05:53 -0400 (Fri, 01 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 nebbiolo1


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 1823/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.14.2  (landing page)
Wanding Zhou
Snapshot Date: 2022-06-30 13:55:04 -0400 (Thu, 30 Jun 2022)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_15
git_last_commit: 67b0bdb
git_last_commit_date: 2022-05-17 20:40:09 -0400 (Tue, 17 May 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: sesame
Version: 1.14.2
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings sesame_1.14.2.tar.gz
StartedAt: 2022-06-30 21:57:14 -0400 (Thu, 30 Jun 2022)
EndedAt: 2022-06-30 22:14:04 -0400 (Thu, 30 Jun 2022)
EllapsedTime: 1010.7 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings sesame_1.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/sesame.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (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 ‘1.14.2’
* 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 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
DMR                         33.186  1.868  35.899
sesameQC_plotHeatSNPs       33.434  1.192  34.789
sesameQC_calcStats          31.143  1.024  32.330
KYCG_plotEnrichAll          28.743  3.152  33.518
inferSpecies                23.313  2.056  26.027
DML                         23.898  1.292  25.698
dyeBiasCorrMostBalanced     19.602  1.268  21.455
sesameQC_plotBetaByDesign   17.293  0.404  17.697
KYCG_plotMeta               16.572  1.036  18.103
getSexInfo                  15.010  0.945  16.875
diffRefSet                  14.361  1.092  15.787
matchDesign                 13.944  0.856  15.054
probeSuccessRate            13.616  1.096  15.714
KYCG_annoProbes             13.390  1.273  15.313
dyeBiasCorr                 13.344  1.085  15.173
KYCG_buildGeneDBs           12.863  1.480  14.767
sesameQC_plotBar            13.483  0.636  14.535
KYCG_plotMetaEnrichment     12.673  0.836  14.100
compareMouseTissueReference 11.544  1.040  13.018
prepSesame                  11.416  1.020  13.019
getRefSet                   11.422  0.875  12.630
compareMouseStrainReference 11.612  0.640  12.584
inferStrain                 11.212  1.013  12.745
testEnrichmentGSEA          11.031  0.983  12.690
testEnrichment              10.103  0.913  11.956
dbStats                      9.704  1.068  11.191
controls                     9.746  0.828  11.420
visualizeGene                8.918  0.900  10.396
detectionIB                  8.346  0.741   9.335
inferTissue                  7.533  1.012   8.869
detectionPnegEcdf            7.899  0.519   8.745
mapToMammal40                7.604  0.588   9.101
formatVCF                    7.304  0.574  10.176
openSesame                   6.877  0.750   8.051
estimateLeukocyte            6.876  0.632   7.838
inferSex                     6.662  0.492   7.588
noMasked                     6.356  0.577   7.345
createUCSCtrack              6.171  0.592   7.091
sdf_read_table               6.095  0.356   6.704
predictAgeHorvath353         5.655  0.716   6.805
scrubSoft                    6.093  0.204   6.297
deidentify                   5.626  0.515   6.566
bisConversionControl         5.376  0.451   6.257
print.DMLSummary             5.267  0.443   6.214
inferEthnicity               5.044  0.543   5.752
dyeBiasNL                    5.073  0.404   5.730
predictAgeSkinBlood          4.862  0.544   5.823
inferSexKaryotypes           4.895  0.352   5.501
summaryExtractTest           4.757  0.450   5.623
scrub                        4.739  0.400   5.139
openSesameToFile             4.789  0.301   5.089
reIdentify                   4.636  0.428   5.328
visualizeProbes              4.520  0.539   5.313
predictMouseAgeInMonth       4.134  0.520   5.177
sesameQC_rankStats           4.073  0.460   5.039
* 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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, 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 
 30.787   2.580  34.275 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0010.0000.000
DML23.898 1.29225.698
DMR33.186 1.86835.899
KYCG_annoProbes13.390 1.27315.313
KYCG_buildGeneDBs12.863 1.48014.767
KYCG_getDBs3.0410.3523.724
KYCG_listDBGroups0.0270.0080.035
KYCG_plotBar0.2870.0560.343
KYCG_plotDot0.2110.0400.251
KYCG_plotEnrichAll28.743 3.15233.518
KYCG_plotLollipop0.1440.0040.148
KYCG_plotManhattan1.3780.0721.449
KYCG_plotMeta16.572 1.03618.103
KYCG_plotMetaEnrichment12.673 0.83614.100
KYCG_plotPointRange3.9130.3874.462
KYCG_plotVolcano0.1510.0080.158
KYCG_plotWaterfall2.7470.2593.261
MValueToBetaValue000
SigDF0.2720.0610.497
addMask0.2790.0480.327
aggregateTestEnrichments1.8340.1441.978
bisConversionControl5.3760.4516.257
checkLevels3.7470.5174.531
cnSegmentation0.2680.0400.560
compareMouseStrainReference11.612 0.64012.584
compareMouseTissueReference11.544 1.04013.018
controls 9.746 0.82811.420
createUCSCtrack6.1710.5927.091
dataFrame2sesameQC1.1640.1681.600
dbStats 9.704 1.06811.191
deidentify5.6260.5156.566
detectionIB8.3460.7419.335
detectionPnegEcdf7.8990.5198.745
diffRefSet14.361 1.09215.787
dmContrasts2.6600.3563.189
dyeBiasCorr13.344 1.08515.173
dyeBiasCorrMostBalanced19.602 1.26821.455
dyeBiasL2.9140.3603.437
dyeBiasNL5.0730.4045.730
estimateLeukocyte6.8760.6327.838
formatVCF 7.304 0.57410.176
getAFTypeIbySumAlleles1.4550.2402.130
getAFs1.1870.1841.639
getBetas0.9570.1391.260
getRefSet11.422 0.87512.630
getSexInfo15.010 0.94516.875
inferEthnicity5.0440.5435.752
inferInfiniumIChannel0.3390.6681.007
inferSex6.6620.4927.588
inferSexKaryotypes4.8950.3525.501
inferSpecies23.313 2.05626.027
inferStrain11.212 1.01312.745
inferTissue7.5331.0128.869
initFileSet1.1450.0721.488
listAvailableMasks1.6860.1592.097
mapFileSet0.0300.0040.034
mapToMammal407.6040.5889.101
matchDesign13.944 0.85615.054
meanIntensity2.8780.3683.667
medianTotalIntensity1.1250.1391.517
noMasked6.3560.5777.345
noob3.6640.3163.980
openSesame6.8770.7508.051
openSesameToFile4.7890.3015.089
pOOBAH3.2280.1803.408
palgen0.0410.0190.061
parseGEOsignalMU0.6710.0910.763
predictAgeHorvath3535.6550.7166.805
predictAgeSkinBlood4.8620.5445.823
predictMouseAgeInMonth4.1340.5205.177
prefixMask1.7730.1602.097
prefixMaskButC0.1020.0000.103
prefixMaskButCG0.0350.0120.046
prepSesame11.416 1.02013.019
prepSesameList0.0020.0000.002
print.DMLSummary5.2670.4436.214
print.fileSet1.2080.1161.488
probeID_designType0.0000.0000.001
probeSuccessRate13.616 1.09615.714
qualityMask3.3170.2293.708
reIdentify4.6360.4285.328
readFileSet0.0560.0000.055
readIDATpair0.1420.0000.142
resetMask0.4200.0440.731
scrub4.7390.4005.139
scrubSoft6.0930.2046.297
sdfPlatform1.0710.1161.451
sdf_read_table6.0950.3566.704
sdf_write_table2.4730.1312.863
searchIDATprefixes0.0060.0050.011
sesame-package3.4630.3764.099
sesameAnno_download000
sesameAnno_get0.0000.0000.001
sesameAnno_getManifestDF0.0000.0000.001
sesameData_getAnno0.0010.0000.000
sesameQC_calcStats31.143 1.02432.330
sesameQC_getStats2.900.042.94
sesameQC_plotBar13.483 0.63614.535
sesameQC_plotBetaByDesign17.293 0.40417.697
sesameQC_plotHeatSNPs33.434 1.19234.789
sesameQC_plotIntensVsBetas2.3420.2282.840
sesameQC_plotRedGrnQQ1.9760.2082.450
sesameQC_rankStats4.0730.4605.039
setMask0.1390.0040.144
signalMU1.1490.1161.429
sliceFileSet0.0340.0010.035
summaryExtractTest4.7570.4505.623
testEnrichment10.103 0.91311.956
testEnrichmentGSEA11.031 0.98312.690
totalIntensities2.7590.2413.418
updateSigDF3.2230.3684.125
visualizeGene 8.918 0.90010.396
visualizeProbes4.5200.5395.313
visualizeRegion2.3760.2922.668
visualizeSegments1.8660.1892.217