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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 1938/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.24.0  (landing page)
Wanding Zhou
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_20
git_last_commit: e86f791
git_last_commit_date: 2024-10-29 10:29:34 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for sesame on palomino8

To the developers/maintainers of the sesame package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: sesame
Version: 1.24.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sesame.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings sesame_1.24.0.tar.gz
StartedAt: 2024-12-20 05:57:25 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 06:16:49 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 1164.7 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sesame.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings sesame_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'sesame/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sesame' version '1.24.0'
* 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 code 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 whether startup messages can be suppressed ... 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
testEnrichmentGene            49.53   3.12   54.47
imputeBetasByGenomicNeighbors 45.36   1.96   48.45
sesameQC_calcStats            31.47   2.80   34.26
inferSex                      29.70   1.50   31.20
sesameQC_plotHeatSNPs         26.53   2.06   28.59
KYCG_plotMeta                 25.88   1.00   27.54
imputeBetas                   21.06   2.24   25.42
KYCG_plotEnrichAll            21.01   1.22   23.51
ELBAR                         19.37   1.73   21.25
sdf_read_table                18.77   0.49   19.28
matchDesign                   17.41   1.09   18.54
sesameQC_plotBar              17.41   0.87   19.31
sesameQC_plotBetaByDesign     16.29   1.96   18.33
diffRefSet                    16.69   0.51   18.13
inferSpecies                  15.46   1.01   16.85
compareMouseStrainReference   15.53   0.81   16.44
KYCG_annoProbes               14.80   0.75   15.90
KYCG_plotMetaEnrichment       14.42   0.77   15.18
visualizeGene                 13.31   0.86   14.20
getRefSet                     13.24   0.61   13.86
testEnrichmentSEA             12.53   1.22   13.74
compareReference              13.04   0.64   13.68
DML                           11.61   1.88   13.55
sdf_write_table               11.64   0.26   11.90
inferStrain                   10.64   1.17   11.79
KYCG_buildGeneDBs             10.94   0.43   12.77
inferTissue                    9.08   1.03   10.09
DMR                            9.36   0.34    9.85
estimateLeukocyte              8.85   0.50    9.61
dbStats                        8.23   0.97    9.55
getMask                        7.27   0.80    8.18
createUCSCtrack                7.43   0.53    8.18
openSesame                     6.71   0.86    7.62
dyeBiasNL                      6.94   0.45    7.41
KYCG_plotSetEnrichment         6.65   0.69    7.42
testEnrichment                 6.44   0.67    7.17
dyeBiasCorrMostBalanced        6.69   0.36    8.14
deidentify                     5.97   0.59    6.64
probeSuccessRate               6.11   0.44    6.55
bisConversionControl           5.97   0.33    6.75
scrubSoft                      5.14   0.81    5.95
noMasked                       4.89   0.48    5.34
sesameQC_rankStats             4.66   0.59    5.26
prepSesame                     4.66   0.56    5.23
parseGEOsignalMU               4.45   0.67    5.11
updateSigDF                    4.15   0.44    5.25
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, saveRDS, setdiff, 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 5 ]
> 
> proc.time()
   user  system elapsed 
  25.73    2.65   28.60 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML11.61 1.8813.55
DMLpredict1.460.191.64
DMR9.360.349.85
ELBAR19.37 1.7321.25
KYCG_annoProbes14.80 0.7515.90
KYCG_buildGeneDBs10.94 0.4312.77
KYCG_getDBs2.760.213.03
KYCG_listDBGroups0.030.000.22
KYCG_loadDBs000
KYCG_plotBar0.660.020.92
KYCG_plotDot0.410.000.41
KYCG_plotEnrichAll21.01 1.2223.51
KYCG_plotLollipop0.20.00.2
KYCG_plotManhattan1.720.031.75
KYCG_plotMeta25.88 1.0027.54
KYCG_plotMetaEnrichment14.42 0.7715.18
KYCG_plotPointRange2.940.183.13
KYCG_plotSetEnrichment6.650.697.42
KYCG_plotVolcano0.160.000.16
KYCG_plotWaterfall3.270.333.62
MValueToBetaValue000
SigDF0.340.110.45
addMask0.090.000.10
aggregateTestEnrichments2.970.153.12
betasCollapseToPfx0.020.000.02
bisConversionControl5.970.336.75
calcEffectSize1.450.241.70
checkLevels3.800.234.17
cnSegmentation0.360.050.41
compareMouseStrainReference15.53 0.8116.44
compareMouseTissueReference000
compareReference13.04 0.6413.68
controls2.390.412.79
createUCSCtrack7.430.538.18
dbStats8.230.979.55
deidentify5.970.596.64
detectionPnegEcdf3.970.244.20
diffRefSet16.69 0.5118.13
dmContrasts2.150.222.37
dyeBiasCorr3.110.363.46
dyeBiasCorrMostBalanced6.690.368.14
dyeBiasL2.920.203.14
dyeBiasNL6.940.457.41
estimateLeukocyte8.850.509.61
formatVCF2.260.422.68
getAFTypeIbySumAlleles1.820.332.16
getAFs1.320.221.55
getBetas1.140.121.27
getMask7.270.808.18
getRefSet13.24 0.6113.86
imputeBetas21.06 2.2425.42
imputeBetasByGenomicNeighbors45.36 1.9648.45
imputeBetasMatrixByMean000
inferEthnicity000
inferInfiniumIChannel0.590.431.02
inferSex29.7 1.531.2
inferSpecies15.46 1.0116.85
inferStrain10.64 1.1711.79
inferTissue 9.08 1.0310.09
initFileSet1.370.241.59
listAvailableMasks1.670.141.82
mLiftOver000
mapFileSet0.040.000.07
mapToMammal403.230.523.85
matchDesign17.41 1.0918.54
meanIntensity3.280.453.74
medianTotalIntensity1.080.211.28
noMasked4.890.485.34
noob3.430.333.77
openSesame6.710.867.62
openSesameToFile2.330.182.52
pOOBAH1.980.132.11
palgen0.050.020.23
parseGEOsignalMU4.450.675.11
predictAge2.610.152.80
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.550.020.56
prefixMaskButC0.190.000.19
prefixMaskButCG0.050.000.05
prepSesame4.660.565.23
prepSesameList000
print.DMLSummary3.730.474.19
print.fileSet1.170.251.42
probeID_designType000
probeSuccessRate6.110.446.55
qualityMask2.680.262.95
reIdentify4.680.104.78
readFileSet0.070.010.08
readIDATpair0.140.000.14
recommendedMaskNames000
resetMask0.520.050.56
scrub3.950.694.64
scrubSoft5.140.815.95
sdfPlatform0.360.060.43
sdf_read_table18.77 0.4919.28
sdf_write_table11.64 0.2611.90
searchIDATprefixes000
sesame-package2.660.312.97
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_readManifestTSV000
sesameQC_calcStats31.47 2.8034.26
sesameQC_getStats2.810.162.99
sesameQC_plotBar17.41 0.8719.31
sesameQC_plotBetaByDesign16.29 1.9618.33
sesameQC_plotHeatSNPs26.53 2.0628.59
sesameQC_plotIntensVsBetas2.640.443.10
sesameQC_plotRedGrnQQ1.360.231.59
sesameQC_rankStats4.660.595.26
sesameQCtoDF3.640.273.90
sesame_checkVersion0.020.000.01
sesamize000
setMask0.120.030.16
signalMU0.880.131.00
sliceFileSet0.030.000.04
summaryExtractTest3.040.363.41
testEnrichment6.440.677.17
testEnrichmentGene49.53 3.1254.47
testEnrichmentSEA12.53 1.2213.74
totalIntensities3.650.343.98
updateSigDF4.150.445.25
visualizeGene13.31 0.8614.20
visualizeProbes1.960.021.97
visualizeRegion0.310.000.31
visualizeSegments2.670.112.79