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This page was generated on 2022-01-21 13:08:31 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 machv2


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? here 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 1775/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.12.7  (landing page)
Wanding Zhou
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_14
git_last_commit: 1e3ec3a
git_last_commit_date: 2021-12-13 15:25:11 -0500 (Mon, 13 Dec 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: sesame
Version: 1.12.7
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_1.12.7.tar.gz
StartedAt: 2022-01-20 18:04:30 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 18:27:10 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 1360.1 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_1.12.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/sesame.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.12.7’
* 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
visualizeSegments            83.490  3.156  87.862
cnSegmentation               81.419  2.633  84.899
DMR                          46.089  0.816  48.139
bSubMostVariable             36.913  0.438  37.644
testEnrichment               35.113  1.644  38.486
compareMouseTissueReference  27.432  0.610  28.718
compareMouseStrainReference  25.312  0.221  27.041
diffRefSet                   24.746  0.426  25.830
testEnrichmentGene           22.219  0.900  24.055
createUCSCtrack              21.613  0.267  22.439
getProbesByChromosome        20.240  0.198  20.789
DML                          17.284  0.921  19.227
visualizeGene                16.778  0.437  18.186
bSubProbes                   15.606  0.346  16.523
print.DMLSummary             15.768  0.146  16.480
reIdentify                   15.124  0.488  16.379
print.sesameQC               14.501  1.026  15.795
as.data.frame.sesameQC       14.231  1.269  15.803
attachManifest               15.166  0.286  16.014
deidentify                   14.997  0.206  15.812
sdf_read_table               14.657  0.463  15.671
getRefSet                    14.828  0.113  15.210
summaryExtractTest           14.381  0.138  15.187
dmContrasts                  14.158  0.309  14.855
bisConversionControl         13.958  0.386  15.312
getDatabaseSetOverlap        13.533  0.284  14.945
getProbesByGene              13.227  0.178  13.932
calcDatabaseSetStatisticsAll 12.411  0.596  15.399
inferTissue                  12.653  0.348  14.989
estimateLeukocyte            12.520  0.278  13.378
sesameQC                     11.430  1.153  12.839
inferStrain                  11.096  0.426  12.431
dyeBiasCorrMostBalanced      11.043  0.297  11.986
SNPcheck                     10.276  0.397  11.390
getSexInfo                    8.375  0.239   8.955
getProbesByRegion             8.253  0.115   8.762
inferSex                      7.930  0.382   8.966
getNormCtls                   7.593  0.160   8.352
qualityRank                   7.503  0.207   8.507
setMaskBySpecies              7.408  0.181   8.258
qualityMask                   7.344  0.205   8.222
bSubComplete                  7.198  0.165   7.619
getAutosomeProbes             6.932  0.091   7.390
totalIntensities              6.591  0.208   7.458
dyeBiasCorr                   6.243  0.191   7.047
dyeBiasCorrTypeINorm          5.496  0.532   6.311
probeSuccessRate              5.800  0.190   6.602
controls                      5.678  0.149   6.605
SigDF                         5.603  0.136   6.289
sdf_write_table               4.707  0.189   5.183
getAFTypeIbySumAlleles        4.684  0.141   5.429
predictMouseAgeInMonth        4.649  0.135   6.781
formatVCF                     4.242  0.160   6.420
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 required package: rmarkdown
Loading sesameData.

----------------------------------------------------------
| SEnsible Step-wise Analysis of DNA MEthylation (SeSAMe)
| --------------------------------------------------------
| Please cache the annotation data for your array platform
| (e.g. EPIC) by calling "sesameDataCache("EPIC")"
| or "sesameDataCacheAll()". 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 
 25.056   1.433  27.212 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0000.0010.000
DML17.284 0.92119.227
DMR46.089 0.81648.139
MValueToBetaValue000
RGChannelSetToSigDFs0.0000.0000.001
SNPcheck10.276 0.39711.390
SigDF5.6030.1366.289
SigDFToRatioSet0.0010.0000.000
SigDFsToRGChannelSet0.0010.0010.000
addMask0.1430.0010.145
as.data.frame.sesameQC14.231 1.26915.803
attachManifest15.166 0.28616.014
bSubComplete7.1980.1657.619
bSubMostVariable36.913 0.43837.644
bSubProbes15.606 0.34616.523
bisConversionControl13.958 0.38615.312
calcDatabaseSetStatisticsAll12.411 0.59615.399
checkLevels1.1250.0543.214
cnSegmentation81.419 2.63384.899
compareDatbaseSetOverlap3.8930.0874.379
compareMouseStrainReference25.312 0.22127.041
compareMouseTissueReference27.432 0.61028.718
controls5.6780.1496.605
createDatabaseSetNetwork4.1480.0934.611
createUCSCtrack21.613 0.26722.439
deidentify14.997 0.20615.812
detectionPnegEcdf0.3340.0070.341
detectionPoobEcdf1.6520.0381.691
detectionPoobEcdf21.6860.0991.786
diffRefSet24.746 0.42625.830
dmContrasts14.158 0.30914.855
dyeBiasCorr6.2430.1917.047
dyeBiasCorrMostBalanced11.043 0.29711.986
dyeBiasCorrTypeINorm5.4960.5326.311
dyeBiasDistortion1.5290.1481.678
estimateLeukocyte12.520 0.27813.378
formatVCF4.2420.1606.420
getAFTypeIbySumAlleles4.6840.1415.429
getAutosomeProbes6.9320.0917.390
getBetas4.0260.1224.430
getDatabaseSetOverlap13.533 0.28414.945
getNormCtls7.5930.1608.352
getProbesByChromosome20.240 0.19820.789
getProbesByGene13.227 0.17813.932
getProbesByRegion8.2530.1158.762
getProbesByTSS0.3560.0000.356
getRefSet14.828 0.11315.210
getSexInfo8.3750.2398.955
inferEthnicity1.3810.0391.422
inferInfiniumIChannel0.3140.0070.321
inferSex7.9300.3828.966
inferSexKaryotypes3.7430.1704.185
inferSpecies0.0010.0010.001
inferStrain11.096 0.42612.431
inferTissue12.653 0.34814.989
initFileSet0.0590.0040.062
mapFileSet0.0690.0050.074
meanIntensity2.4950.0813.028
medianTotalIntensity2.3580.0982.812
neob2.5550.2122.767
noMasked2.3800.1122.752
noob3.5770.3463.925
openSesame1.7080.0221.732
openSesameToFile2.4120.1882.605
plotLollipop1.2640.0361.301
plotVolcano0.1980.0020.200
predictAgeHorvath3534.4450.0874.928
predictAgeSkinBlood0.1940.0010.195
predictMouseAgeInMonth4.6490.1356.781
print.DMLSummary15.768 0.14616.480
print.SigDF1.6690.0372.039
print.fileSet0.0560.0030.058
print.sesameQC14.501 1.02615.795
probeID_designType0.0000.0010.001
probeSuccessRate5.8000.1906.602
qualityMask7.3440.2058.222
qualityRank7.5030.2078.507
reIdentify15.124 0.48816.379
readFileSet0.0950.0040.099
readIDATpair0.1690.0020.170
resetMask1.2550.0371.674
scrub2.1950.3612.557
scrubSoft3.6940.7244.423
sdfPlatform0.8750.0481.227
sdf_read_table14.657 0.46315.671
sdf_write_table4.7070.1895.183
searchIDATprefixes0.0060.0020.008
sesame-package0.8950.0050.899
sesamePlotIntensVsBetas3.2850.1583.753
sesamePlotRedGrnQQ2.6440.4833.518
sesameQC11.430 1.15312.839
sesamize000
setMask3.9950.1904.449
setMaskBySpecies7.4080.1818.258
signalMU1.7340.0432.031
sliceFileSet3.8800.2184.485
summaryExtractTest14.381 0.13815.187
testEnrichment35.113 1.64438.486
testEnrichmentGene22.219 0.90024.055
totalIntensities6.5910.2087.458
visualizeGene16.778 0.43718.186
visualizeProbes1.6950.0101.708
visualizeRegion0.8600.0090.871
visualizeSegments83.490 3.15687.862