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This page was generated on 2024-03-04 11:37:51 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 1934/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.20.0  (landing page)
Wanding Zhou
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_18
git_last_commit: a980995
git_last_commit_date: 2023-10-24 11:06:17 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 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 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for sesame on lconway


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: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2024-03-03 23:26:55 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 23:44:34 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 1059.8 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/sesame.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.20.0’
* 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 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 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          126.297  5.667 134.786
sesameQC_calcStats           24.795  2.163  27.154
KYCG_plotMeta                24.229  1.060  25.632
KYCG_plotEnrichAll           20.514  1.062  22.164
sesameQC_plotHeatSNPs        19.894  1.551  21.816
ELBAR                        16.903  3.266  20.441
inferSpecies                 17.111  0.791  18.273
convertTo                    15.089  0.399  15.666
KYCG_annoProbes              14.351  0.875  15.501
testEnrichmentSEA            13.677  1.171  15.343
matchDesign                  13.833  0.824  14.802
sesameQC_plotBar             13.531  0.567  14.352
diffRefSet                   13.246  0.572  14.054
compareMouseStrainReference  13.343  0.410  13.987
sesameQC_plotBetaByDesign    11.814  1.619  13.504
getRefSet                    12.737  0.613  13.511
inferTissue                  10.851  1.554  12.869
compareReference             11.668  0.647  12.588
KYCG_plotMetaEnrichment      11.266  0.608  12.144
KYCG_buildGeneDBs            11.281  0.485  11.989
visualizeGene                10.555  0.547  11.448
getSexInfo                    9.877  0.633  10.904
DML                           8.953  1.355  10.799
DMR                           9.500  0.386  10.174
sdf_read_table                9.159  0.423   9.758
inferStrain                   8.471  0.758   9.403
estimateLeukocyte             8.135  0.598   8.886
dbStats                       7.246  0.747   8.144
createUCSCtrack               7.501  0.327   7.971
dyeBiasNL                     6.862  0.609   7.605
dyeBiasCorrMostBalanced       6.995  0.302   7.490
testEnrichment                6.233  0.846   7.269
KYCG_plotSetEnrichment        6.391  0.623   7.185
openSesame                    5.753  1.149   7.044
probeSuccessRate              6.416  0.469   7.188
deidentify                    6.382  0.363   6.993
getMask                       5.727  0.411   6.328
bisConversionControl          5.558  0.273   6.164
inferSex                      5.060  0.482   5.673
reIdentify                    5.148  0.375   5.620
* 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/4.3-x86_64/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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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, 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, 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 
 22.764   1.907  24.902 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0000.0000.001
DML 8.953 1.35510.799
DMLpredict1.4410.1221.639
DMR 9.500 0.38610.174
ELBAR16.903 3.26620.441
KYCG_annoProbes14.351 0.87515.501
KYCG_buildGeneDBs11.281 0.48511.989
KYCG_getDBs3.1040.2643.501
KYCG_listDBGroups0.0360.0020.037
KYCG_loadDBs0.0000.0010.001
KYCG_plotBar0.2260.0160.243
KYCG_plotDot0.5910.0600.659
KYCG_plotEnrichAll20.514 1.06222.164
KYCG_plotLollipop0.1560.0010.158
KYCG_plotManhattan1.5320.3361.888
KYCG_plotMeta24.229 1.06025.632
KYCG_plotMetaEnrichment11.266 0.60812.144
KYCG_plotPointRange3.9820.2884.387
KYCG_plotSetEnrichment6.3910.6237.185
KYCG_plotVolcano0.1560.0050.163
KYCG_plotWaterfall3.0600.1863.313
MValueToBetaValue000
SigDF0.5630.1100.728
addMask0.1060.0010.107
aggregateTestEnrichments2.0540.0742.136
betasCollapseToPfx0.0020.0000.002
bisConversionControl5.5580.2736.164
calcEffectSize1.6310.1411.835
checkLevels3.2030.3113.756
cnSegmentation0.3220.0650.540
compareMouseStrainReference13.343 0.41013.987
compareMouseTissueReference0.0000.0010.000
compareReference11.668 0.64712.588
controls2.2020.2042.522
convertTo15.089 0.39915.666
createUCSCtrack7.5010.3277.971
dataFrame2sesameQC1.0430.1061.302
dbStats7.2460.7478.144
deidentify6.3820.3636.993
detectionPnegEcdf3.2570.1923.521
diffRefSet13.246 0.57214.054
dmContrasts2.3650.3532.783
dyeBiasCorr3.0120.2343.363
dyeBiasCorrMostBalanced6.9950.3027.490
dyeBiasL2.4690.1432.676
dyeBiasNL6.8620.6097.605
estimateLeukocyte8.1350.5988.886
formatVCF2.1910.2372.769
getAFTypeIbySumAlleles2.1150.2432.486
getAFs1.3740.1121.549
getBetas0.9840.0931.135
getMask5.7270.4116.328
getRefSet12.737 0.61313.511
getSexInfo 9.877 0.63310.904
imputeTo1.8860.2132.163
inferEthnicity2.2700.1952.761
inferInfiniumIChannel0.5430.6191.222
inferSex5.0600.4825.673
inferSexKaryotypes3.6100.2854.068
inferSpecies17.111 0.79118.273
inferStrain8.4710.7589.403
inferTissue10.851 1.55412.869
initFileSet1.3400.2321.644
listAvailableMasks2.0130.1672.245
mapFileSet0.0420.0030.046
mapToMammal403.8720.3504.402
matchDesign13.833 0.82414.802
meanIntensity2.8760.1773.171
medianTotalIntensity0.9930.0671.125
noMasked2.5770.7313.378
noob2.2230.0512.286
openSesame5.7531.1497.044
openSesameToFile1.5930.0381.651
pOOBAH1.5010.0121.523
palgen0.0480.0100.059
parseGEOsignalMU3.0940.1713.345
predictAge2.7380.1412.945
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth0.0000.0010.000
prefixMask0.8260.5491.397
prefixMaskButC0.1260.0000.127
prefixMaskButCG0.0500.0000.051
prepSesame3.7450.1884.004
prepSesameList0.0010.0010.002
print.DMLSummary3.1560.8134.094
print.fileSet1.3260.1961.693
probeID_designType0.0010.0010.001
probeSuccessRate6.4160.4697.188
qualityMask3.4150.2363.772
reIdentify5.1480.3755.620
readFileSet0.0670.0060.073
readIDATpair0.1660.0040.170
recommendedMaskNames000
resetMask0.4250.0490.528
scrub2.4630.2352.709
scrubSoft3.6890.6724.387
sdfPlatform0.3010.0720.430
sdf_read_table9.1590.4239.758
sdf_write_table2.8320.1583.068
searchIDATprefixes0.0030.0020.007
sesame-package2.5430.5023.584
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges0.0000.0000.001
sesameAnno_download0.0000.0010.000
sesameAnno_get0.0000.0010.000
sesameAnno_readManifestTSV000
sesameData_getAnno000
sesameQC_calcStats24.795 2.16327.154
sesameQC_getStats2.2110.0202.247
sesameQC_plotBar13.531 0.56714.352
sesameQC_plotBetaByDesign11.814 1.61913.504
sesameQC_plotHeatSNPs19.894 1.55121.816
sesameQC_plotIntensVsBetas2.1480.5092.736
sesameQC_plotRedGrnQQ1.2360.1381.437
sesameQC_rankStats3.7050.4684.300
sesame_checkVersion0.0040.0010.005
sesamize000
setMask0.1180.0020.120
signalMU0.8540.0630.973
sliceFileSet0.0310.0020.033
summaryExtractTest3.1760.7224.072
testEnrichment6.2330.8467.269
testEnrichmentGene126.297 5.667134.786
testEnrichmentSEA13.677 1.17115.343
totalIntensities3.2070.2063.552
updateSigDF4.1160.5244.790
visualizeGene10.555 0.54711.448
visualizeProbes4.5860.1824.840
visualizeRegion0.3860.0030.390
visualizeSegments2.1290.7543.053