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This page was generated on 2022-07-01 12:08:43 -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 merida1


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: /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_1.14.2.tar.gz
StartedAt: 2022-07-01 07:57:22 -0400 (Fri, 01 Jul 2022)
EndedAt: 2022-07-01 08:33:57 -0400 (Fri, 01 Jul 2022)
EllapsedTime: 2194.8 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/sesame.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.14.2’
* 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
sesameQC_calcStats          58.477  2.768  92.369
DMR                         54.576  2.599  61.775
sesameQC_plotHeatSNPs       53.321  2.235  83.251
KYCG_plotEnrichAll          41.380  1.131  46.302
inferSpecies                36.449  1.084  49.566
DML                         35.888  0.922  43.208
dyeBiasCorrMostBalanced     30.177  0.642  47.132
sesameQC_plotBetaByDesign   27.941  1.833  43.851
compareMouseStrainReference 28.384  0.437  37.947
sesameQC_plotBar            26.781  0.843  40.461
KYCG_plotMeta               26.500  0.675  28.789
compareMouseTissueReference 25.988  0.722  35.097
diffRefSet                  24.615  0.760  34.521
matchDesign                 24.583  0.701  33.010
probeSuccessRate            22.708  0.694  33.040
inferStrain                 21.562  0.762  29.111
getSexInfo                  21.712  0.525  29.627
KYCG_plotMetaEnrichment     20.839  1.071  23.957
detectionIB                 19.601  2.107  38.607
KYCG_annoProbes             20.831  0.497  22.834
dyeBiasCorr                 19.470  0.875  40.523
prepSesame                  18.730  0.898  27.939
KYCG_buildGeneDBs           19.009  0.379  20.534
getRefSet                   18.402  0.481  28.323
visualizeGene               16.052  0.587  25.331
testEnrichmentGSEA          15.351  0.835  25.377
controls                    15.209  0.407  20.978
testEnrichment              14.960  0.553  23.895
dbStats                     14.271  0.750  19.675
inferTissue                 12.700  0.962  17.853
deidentify                  13.114  0.239  26.909
estimateLeukocyte           12.286  0.502  20.416
formatVCF                   12.236  0.549  23.011
detectionPnegEcdf           12.290  0.431  24.260
openSesame                  11.925  0.723  16.937
reIdentify                  12.077  0.221  18.256
mapToMammal40               11.658  0.312  15.926
dyeBiasNL                   11.415  0.438  15.700
bisConversionControl        11.251  0.241  15.460
inferSex                    10.904  0.372  14.963
sdf_read_table              10.520  0.447  16.552
scrubSoft                   10.107  0.772  16.234
print.DMLSummary            10.152  0.600  14.378
createUCSCtrack              9.921  0.242  13.722
noMasked                     9.661  0.212  13.658
openSesameToFile             9.605  0.116  12.483
predictAgeHorvath353         8.051  0.842  11.940
visualizeProbes              8.232  0.208  12.912
inferSexKaryotypes           8.082  0.270  10.996
summaryExtractTest           7.446  0.482  12.327
sesameQC_rankStats           7.374  0.427  12.228
scrub                        7.047  0.520  11.165
inferEthnicity               7.179  0.338  10.037
predictAgeSkinBlood          7.047  0.289   9.868
qualityMask                  6.888  0.177  10.229
noob                         6.239  0.521   8.898
sesameQC_getStats            6.336  0.214   9.611
KYCG_plotPointRange          6.352  0.168   8.748
sesame-package               6.274  0.234   9.871
predictMouseAgeInMonth       6.052  0.280   9.126
pOOBAH                       5.669  0.540   7.887
sesameQC_plotIntensVsBetas   5.805  0.353   9.522
updateSigDF                  5.256  0.215   8.346
meanIntensity                4.835  0.475   7.721
sdf_write_table              4.807  0.310   7.668
totalIntensities             4.754  0.229   7.736
KYCG_plotWaterfall           4.778  0.125   6.554
checkLevels                  4.347  0.178   6.020
aggregateTestEnrichments     3.986  0.064   5.366
dmContrasts                  3.589  0.228   6.714
prefixMask                   3.248  0.103   5.218
* 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/4.2/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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 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 
 49.658   2.367  76.878 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0000.0000.003
DML35.888 0.92243.208
DMR54.576 2.59961.775
KYCG_annoProbes20.831 0.49722.834
KYCG_buildGeneDBs19.009 0.37920.534
KYCG_getDBs4.2410.2104.987
KYCG_listDBGroups0.0510.0030.058
KYCG_plotBar0.6450.0570.764
KYCG_plotDot0.5160.0530.586
KYCG_plotEnrichAll41.380 1.13146.302
KYCG_plotLollipop0.2790.0120.309
KYCG_plotManhattan1.7570.0411.855
KYCG_plotMeta26.500 0.67528.789
KYCG_plotMetaEnrichment20.839 1.07123.957
KYCG_plotPointRange6.3520.1688.748
KYCG_plotVolcano0.3150.0020.404
KYCG_plotWaterfall4.7780.1256.554
MValueToBetaValue0.0010.0000.000
SigDF0.4560.0370.875
addMask0.1510.0010.203
aggregateTestEnrichments3.9860.0645.366
bisConversionControl11.251 0.24115.460
checkLevels4.3470.1786.020
cnSegmentation0.4530.0440.762
compareMouseStrainReference28.384 0.43737.947
compareMouseTissueReference25.988 0.72235.097
controls15.209 0.40720.978
createUCSCtrack 9.921 0.24213.722
dataFrame2sesameQC1.7290.1042.545
dbStats14.271 0.75019.675
deidentify13.114 0.23926.909
detectionIB19.601 2.10738.607
detectionPnegEcdf12.290 0.43124.260
diffRefSet24.615 0.76034.521
dmContrasts3.5890.2286.714
dyeBiasCorr19.470 0.87540.523
dyeBiasCorrMostBalanced30.177 0.64247.132
dyeBiasL2.7230.1604.182
dyeBiasNL11.415 0.43815.700
estimateLeukocyte12.286 0.50220.416
formatVCF12.236 0.54923.011
getAFTypeIbySumAlleles2.3900.1694.568
getAFs1.7690.1383.062
getBetas1.1620.0671.921
getRefSet18.402 0.48128.323
getSexInfo21.712 0.52529.627
inferEthnicity 7.179 0.33810.037
inferInfiniumIChannel0.6920.4271.441
inferSex10.904 0.37214.963
inferSexKaryotypes 8.082 0.27010.996
inferSpecies36.449 1.08449.566
inferStrain21.562 0.76229.111
inferTissue12.700 0.96217.853
initFileSet1.8740.2182.790
listAvailableMasks2.6850.0943.877
mapFileSet0.0630.0030.087
mapToMammal4011.658 0.31215.926
matchDesign24.583 0.70133.010
meanIntensity4.8350.4757.721
medianTotalIntensity1.6090.0452.346
noMasked 9.661 0.21213.658
noob6.2390.5218.898
openSesame11.925 0.72316.937
openSesameToFile 9.605 0.11612.483
pOOBAH5.6690.5407.887
palgen0.0750.0170.139
parseGEOsignalMU1.0320.0201.380
predictAgeHorvath353 8.051 0.84211.940
predictAgeSkinBlood7.0470.2899.868
predictMouseAgeInMonth6.0520.2809.126
prefixMask3.2480.1035.218
prefixMaskButC0.3110.0010.438
prefixMaskButCG0.1390.0000.198
prepSesame18.730 0.89827.939
prepSesameList0.0020.0000.003
print.DMLSummary10.152 0.60014.378
print.fileSet2.0010.1783.027
probeID_designType0.0010.0000.001
probeSuccessRate22.708 0.69433.040
qualityMask 6.888 0.17710.229
reIdentify12.077 0.22118.256
readFileSet0.0920.0080.151
readIDATpair0.2420.0040.351
resetMask0.6270.0391.030
scrub 7.047 0.52011.165
scrubSoft10.107 0.77216.234
sdfPlatform2.4540.2314.177
sdf_read_table10.520 0.44716.552
sdf_write_table4.8070.3107.668
searchIDATprefixes0.0060.0030.010
sesame-package6.2740.2349.871
sesameAnno_download000
sesameAnno_get0.0010.0000.000
sesameAnno_getManifestDF0.0010.0000.000
sesameData_getAnno0.0000.0000.001
sesameQC_calcStats58.477 2.76892.369
sesameQC_getStats6.3360.2149.611
sesameQC_plotBar26.781 0.84340.461
sesameQC_plotBetaByDesign27.941 1.83343.851
sesameQC_plotHeatSNPs53.321 2.23583.251
sesameQC_plotIntensVsBetas5.8050.3539.522
sesameQC_plotRedGrnQQ2.2750.2704.014
sesameQC_rankStats 7.374 0.42712.228
setMask0.1750.0010.262
signalMU1.6440.1172.757
sliceFileSet0.0640.0050.102
summaryExtractTest 7.446 0.48212.327
testEnrichment14.960 0.55323.895
testEnrichmentGSEA15.351 0.83525.377
totalIntensities4.7540.2297.736
updateSigDF5.2560.2158.346
visualizeGene16.052 0.58725.331
visualizeProbes 8.232 0.20812.912
visualizeRegion1.3350.0442.107
visualizeSegments2.4110.1433.951