Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-15 11:06:56 -0400 (Mon, 15 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4378
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4161
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4169
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 1820/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.15.6  (landing page)
Wanding Zhou
Snapshot Date: 2022-08-14 14:00:05 -0400 (Sun, 14 Aug 2022)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: master
git_last_commit: 5216376
git_last_commit_date: 2022-07-24 22:27:15 -0400 (Sun, 24 Jul 2022)
nebbiolo2Linux (Ubuntu 20.04.4 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 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: sesame
Version: 1.15.6
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sesame.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings sesame_1.15.6.tar.gz
StartedAt: 2022-08-15 05:52:22 -0400 (Mon, 15 Aug 2022)
EndedAt: 2022-08-15 06:08:20 -0400 (Mon, 15 Aug 2022)
EllapsedTime: 958.2 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 --force-multiarch --install=check:sesame.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings sesame_1.15.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/sesame.Rcheck'
* using R version 4.2.1 (2022-06-23 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 '1.15.6'
* 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          30.65   1.22   33.34
sesameQC_calcStats          28.71   1.11   29.88
sesameQC_plotHeatSNPs       26.75   0.93   27.81
inferSpecies                20.18   0.80   21.79
dyeBiasCorrMostBalanced     19.30   0.57   20.84
matchDesign                 17.46   0.75   18.26
getSexInfo                  15.99   0.53   16.68
DMR                         14.73   0.42   15.79
KYCG_plotMeta               14.31   0.78   15.59
sesameQC_plotBar            14.56   0.42   15.81
sesameQC_plotBetaByDesign   12.89   0.61   13.50
probeSuccessRate            12.54   0.55   13.46
diffRefSet                  12.45   0.47   13.61
KYCG_annoProbes             12.21   0.55   13.21
compareMouseStrainReference 11.75   0.52   12.54
KYCG_buildGeneDBs           11.72   0.37   12.70
inferStrain                 10.90   0.56   11.78
getRefSet                   10.97   0.34   11.50
compareReference            10.61   0.67   11.38
KYCG_plotMetaEnrichment     10.03   0.40   10.57
dyeBiasCorr                  9.84   0.50   11.00
dbStats                      9.67   0.53   10.71
testEnrichment               9.69   0.44   10.33
DML                          8.70   1.41   10.30
sdf_read_table               9.59   0.23    9.89
testEnrichmentSEA            9.14   0.57    9.86
visualizeGene                8.55   0.50    9.25
estimateLeukocyte            8.35   0.42    9.24
controls                     8.09   0.47    8.89
formatVCF                    8.00   0.50    8.69
detectionIB                  7.66   0.64    8.36
inferSex                     7.97   0.25    8.33
openSesame                   7.50   0.39    8.06
prepSesame                   7.15   0.55    7.77
inferTissue                  7.17   0.42    7.67
sdf_write_table              7.41   0.10    7.65
mapToMammal40                6.90   0.41    7.47
detectionPnegEcdf            6.79   0.33    7.22
createUCSCtrack              6.49   0.22    7.17
dyeBiasNL                    6.26   0.36    6.76
noMasked                     5.86   0.17    6.14
openSesameToFile             5.47   0.25    5.72
inferSexKaryotypes           5.45   0.19    5.68
scrubSoft                    5.30   0.31    5.61
bisConversionControl         5.14   0.20    5.64
deidentify                   4.89   0.34    5.33
KYCG_plotSetEnrichment       4.86   0.29    5.31
KYCG_plotPointRange          4.84   0.28    5.16
* 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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/sesame_1.15.6.tar.gz && rm -rf sesame.buildbin-libdir && mkdir sesame.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sesame.buildbin-libdir sesame_1.15.6.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL sesame_1.15.6.zip && rm sesame_1.15.6.tar.gz sesame_1.15.6.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  161k  100  161k    0     0  1654k      0 --:--:-- --:--:-- --:--:-- 1668k
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'sesame' as sesame_1.15.6.zip
* DONE (sesame)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'sesame' successfully unpacked and MD5 sums checked

Tests output

sesame.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 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, 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 
  31.53    3.34   55.12 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML 8.70 1.4110.30
DMLpredict1.230.091.40
DMR14.73 0.4215.79
KYCG_annoProbes12.21 0.5513.21
KYCG_buildGeneDBs11.72 0.3712.70
KYCG_getDBs2.510.333.03
KYCG_listDBGroups0.030.000.05
KYCG_plotBar0.720.000.72
KYCG_plotDot0.240.000.23
KYCG_plotEnrichAll30.65 1.2233.34
KYCG_plotLollipop0.130.000.13
KYCG_plotManhattan1.470.051.51
KYCG_plotMeta14.31 0.7815.59
KYCG_plotMetaEnrichment10.03 0.4010.57
KYCG_plotPointRange4.840.285.16
KYCG_plotSetEnrichment4.860.295.31
KYCG_plotVolcano0.160.000.15
KYCG_plotWaterfall2.440.072.56
MValueToBetaValue000
SigDF0.370.030.52
addMask0.080.000.08
aggregateTestEnrichments1.970.082.05
bisConversionControl5.140.205.64
calcEffectSize1.330.061.42
checkLevels3.080.193.47
cnSegmentation0.280.060.39
compareMouseStrainReference11.75 0.5212.54
compareMouseTissueReference000
compareReference10.61 0.6711.38
controls8.090.478.89
createUCSCtrack6.490.227.17
dataFrame2sesameQC0.920.101.08
dbStats 9.67 0.5310.71
deidentify4.890.345.33
detectionIB7.660.648.36
detectionPnegEcdf6.790.337.22
diffRefSet12.45 0.4713.61
dmContrasts1.720.121.90
dyeBiasCorr 9.84 0.5011.00
dyeBiasCorrMostBalanced19.30 0.5720.84
dyeBiasL1.610.151.80
dyeBiasNL6.260.366.76
estimateLeukocyte8.350.429.24
formatVCF8.000.508.69
getAFTypeIbySumAlleles1.590.101.79
getAFs1.130.091.28
getBetas0.870.131.16
getRefSet10.97 0.3411.50
getSexInfo15.99 0.5316.68
inferEthnicity3.780.143.97
inferInfiniumIChannel0.590.340.94
inferSex7.970.258.33
inferSexKaryotypes5.450.195.68
inferSpecies20.18 0.8021.79
inferStrain10.90 0.5611.78
inferTissue7.170.427.67
initFileSet1.100.161.30
listAvailableMasks1.610.111.78
mapFileSet0.030.000.05
mapToMammal406.900.417.47
matchDesign17.46 0.7518.26
meanIntensity3.050.233.49
medianTotalIntensity1.030.051.11
noMasked5.860.176.14
noob4.280.194.47
openSesame7.500.398.06
openSesameToFile5.470.255.72
pOOBAH3.310.183.50
palgen0.050.040.09
parseGEOsignalMU0.720.030.75
predictAge2.440.152.88
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.430.020.45
prefixMaskButC0.130.000.13
prefixMaskButCG0.050.000.04
prepSesame7.150.557.77
prepSesameList000
print.DMLSummary3.170.123.48
print.fileSet1.040.111.17
probeID_designType000
probeSuccessRate12.54 0.5513.46
qualityMask3.080.063.18
reIdentify4.410.194.65
readFileSet0.060.000.06
readIDATpair0.120.000.12
resetMask0.300.070.42
scrub3.950.164.11
scrubSoft5.300.315.61
sdfPlatform1.050.101.18
sdf_read_table9.590.239.89
sdf_write_table7.410.107.65
searchIDATprefixes0.010.000.02
sesame-package3.430.183.65
sesameAnno_download000
sesameAnno_get000
sesameData_getAnno000
sesameQC_calcStats28.71 1.1129.88
sesameQC_getStats2.850.102.94
sesameQC_plotBar14.56 0.4215.81
sesameQC_plotBetaByDesign12.89 0.6113.50
sesameQC_plotHeatSNPs26.75 0.9327.81
sesameQC_plotIntensVsBetas2.130.162.33
sesameQC_plotRedGrnQQ1.200.081.31
sesameQC_rankStats3.500.364.00
setMask0.090.000.10
signalMU0.830.060.93
sliceFileSet0.030.000.05
summaryExtractTest2.670.443.20
testEnrichment 9.69 0.4410.33
testEnrichmentSEA9.140.579.86
totalIntensities2.930.183.28
updateSigDF2.700.293.30
visualizeGene8.550.509.25
visualizeProbes4.490.214.76
visualizeRegion0.460.030.50
visualizeSegments2.770.012.83