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This page was generated on 2025-02-13 12:13 -0500 (Thu, 13 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4754
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4502
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4525
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4477
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4414
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: 2025-02-10 13:00 -0500 (Mon, 10 Feb 2025)
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    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for sesame on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: sesame
Version: 1.24.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sesame_1.24.0.tar.gz
StartedAt: 2025-02-11 10:23:16 -0000 (Tue, 11 Feb 2025)
EndedAt: 2025-02-11 10:39:04 -0000 (Tue, 11 Feb 2025)
EllapsedTime: 947.4 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sesame_1.24.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* 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 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 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 loading without being on the library search path ... 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            43.141  0.721  43.994
imputeBetasByGenomicNeighbors 38.995  0.539  39.834
inferSex                      25.655  0.239  25.937
imputeBetas                   23.199  0.407  23.861
sesameQC_plotHeatSNPs         23.130  0.268  23.444
sesameQC_calcStats            23.128  0.147  23.312
KYCG_plotMeta                 22.988  0.148  23.244
KYCG_plotEnrichAll            20.366  0.562  21.023
ELBAR                         16.620  0.268  16.964
matchDesign                   16.194  0.255  16.481
compareMouseStrainReference   15.551  0.108  15.699
inferSpecies                  15.132  0.368  15.531
diffRefSet                    13.982  0.195  14.437
KYCG_annoProbes               13.999  0.175  14.325
compareReference              13.931  0.199  14.161
sesameQC_plotBetaByDesign     12.773  0.040  12.840
KYCG_plotMetaEnrichment       12.099  0.187  12.322
sesameQC_plotBar              11.872  0.144  12.047
getRefSet                     11.652  0.148  11.830
testEnrichmentSEA             11.626  0.160  11.812
KYCG_buildGeneDBs             10.625  0.211  10.869
visualizeGene                  9.455  0.108   9.587
DML                            9.133  0.351   9.599
DMR                            9.029  0.310   9.526
inferStrain                    8.623  0.243   8.895
sdf_read_table                 8.167  0.124   8.303
inferTissue                    7.650  0.156   7.823
KYCG_plotSetEnrichment         7.460  0.096   7.581
dyeBiasNL                      6.986  0.100   7.114
dbStats                        6.947  0.124   7.120
estimateLeukocyte              6.820  0.215   7.061
getMask                        6.638  0.139   6.805
deidentify                     6.488  0.087   6.612
dyeBiasCorrMostBalanced        6.130  0.191   6.347
bisConversionControl           6.024  0.107   6.155
createUCSCtrack                6.040  0.076   6.129
openSesame                     5.709  0.227   5.973
reIdentify                     5.615  0.028   5.653
testEnrichment                 5.417  0.132   5.560
probeSuccessRate               5.400  0.084   5.494
* 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.2/site-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) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
 20.579   0.695  21.310 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML9.1330.3519.599
DMLpredict1.4710.0271.506
DMR9.0290.3109.526
ELBAR16.620 0.26816.964
KYCG_annoProbes13.999 0.17514.325
KYCG_buildGeneDBs10.625 0.21110.869
KYCG_getDBs3.0610.0953.169
KYCG_listDBGroups0.0390.0000.039
KYCG_loadDBs000
KYCG_plotBar0.2450.0240.270
KYCG_plotDot0.9190.0200.941
KYCG_plotEnrichAll20.366 0.56221.023
KYCG_plotLollipop0.2110.0000.212
KYCG_plotManhattan1.3350.0001.338
KYCG_plotMeta22.988 0.14823.244
KYCG_plotMetaEnrichment12.099 0.18712.322
KYCG_plotPointRange2.4800.0642.557
KYCG_plotSetEnrichment7.4600.0967.581
KYCG_plotVolcano0.1980.0000.198
KYCG_plotWaterfall3.1230.0283.161
MValueToBetaValue000
SigDF0.3710.0200.392
addMask0.1120.0000.112
aggregateTestEnrichments2.4600.0402.506
betasCollapseToPfx0.0180.0000.017
bisConversionControl6.0240.1076.155
calcEffectSize1.3120.0241.339
checkLevels3.1810.0723.263
cnSegmentation0.3630.0040.368
compareMouseStrainReference15.551 0.10815.699
compareMouseTissueReference0.0010.0000.000
compareReference13.931 0.19914.161
controls2.1490.0642.217
createUCSCtrack6.0400.0766.129
dbStats6.9470.1247.120
deidentify6.4880.0876.612
detectionPnegEcdf2.8250.0402.947
diffRefSet13.982 0.19514.437
dmContrasts2.1140.0402.161
dyeBiasCorr3.0630.0603.132
dyeBiasCorrMostBalanced6.1300.1916.347
dyeBiasL3.1940.0523.253
dyeBiasNL6.9860.1007.114
estimateLeukocyte6.8200.2157.061
formatVCF2.1950.0562.257
getAFTypeIbySumAlleles1.9280.0481.983
getAFs1.2920.0161.312
getBetas1.0150.0161.033
getMask6.6380.1396.805
getRefSet11.652 0.14811.830
imputeBetas23.199 0.40723.861
imputeBetasByGenomicNeighbors38.995 0.53939.834
imputeBetasMatrixByMean0.0010.0000.002
inferEthnicity0.0010.0000.001
inferInfiniumIChannel0.3060.0960.401
inferSex25.655 0.23925.937
inferSpecies15.132 0.36815.531
inferStrain8.6230.2438.895
inferTissue7.6500.1567.823
initFileSet1.2290.0401.271
listAvailableMasks1.3220.0231.350
mLiftOver0.0010.0000.000
mapFileSet0.040.000.04
mapToMammal402.7570.0802.848
matchDesign16.194 0.25516.481
meanIntensity2.7580.0842.850
medianTotalIntensity0.8320.0950.930
noMasked3.7270.0683.802
noob2.3090.0482.361
openSesame5.7090.2275.973
openSesameToFile1.6410.0081.659
pOOBAH1.3690.0001.371
palgen0.0480.0000.052
parseGEOsignalMU3.1020.0443.152
predictAge2.2450.0322.280
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth0.0010.0000.000
prefixMask0.5150.0000.515
prefixMaskButC0.1550.0000.156
prefixMaskButCG0.0650.0000.066
prepSesame4.0790.0524.140
prepSesameList0.0010.0000.001
print.DMLSummary3.2900.1203.416
print.fileSet1.2790.0321.314
probeID_designType0.0010.0000.000
probeSuccessRate5.4000.0845.494
qualityMask2.4000.0592.465
reIdentify5.6150.0285.653
readFileSet0.0580.0000.058
readIDATpair0.1260.0000.126
recommendedMaskNames000
resetMask0.5390.0080.548
scrub2.8430.0722.918
scrubSoft4.3810.0164.404
sdfPlatform0.3390.0240.364
sdf_read_table8.1670.1248.303
sdf_write_table2.2850.0602.402
searchIDATprefixes0.0050.0000.009
sesame-package2.2230.0602.291
sesameAnno_attachManifest000
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download0.0010.0000.000
sesameAnno_readManifestTSV000
sesameQC_calcStats23.128 0.14723.312
sesameQC_getStats1.9380.0041.944
sesameQC_plotBar11.872 0.14412.047
sesameQC_plotBetaByDesign12.773 0.04012.840
sesameQC_plotHeatSNPs23.130 0.26823.444
sesameQC_plotIntensVsBetas2.2840.0322.320
sesameQC_plotRedGrnQQ1.5330.0351.572
sesameQC_rankStats4.0770.0604.149
sesameQCtoDF1.9180.0081.929
sesame_checkVersion0.0010.0040.004
sesamize0.0010.0000.000
setMask0.1060.0000.106
signalMU1.1040.0401.147
sliceFileSet0.0370.0000.038
summaryExtractTest2.7280.1522.886
testEnrichment5.4170.1325.560
testEnrichmentGene43.141 0.72143.994
testEnrichmentSEA11.626 0.16011.812
totalIntensities3.1100.0923.210
updateSigDF3.7750.1433.931
visualizeGene9.4550.1089.587
visualizeProbes3.5660.0203.595
visualizeRegion0.4500.0000.452
visualizeSegments2.0230.0682.097