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This page was generated on 2024-05-04 11:41:07 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1952/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.22.0  (landing page)
Wanding Zhou
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_19
git_last_commit: 5afa15d
git_last_commit_date: 2024-04-30 11:07:28 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for sesame on kunpeng2


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: 1.22.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings sesame_1.22.0.tar.gz
StartedAt: 2024-05-04 11:57:21 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 12:18:46 -0000 (Sat, 04 May 2024)
EllapsedTime: 1285.2 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings sesame_1.22.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.22.0’
* 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          125.696  1.832 149.358
inferSex                     43.881  0.902  49.188
sesameQC_calcStats           29.761  0.136  33.027
KYCG_plotMeta                26.035  0.493  29.855
sesameQC_plotHeatSNPs        25.914  0.136  27.690
ELBAR                        23.137  0.466  24.815
KYCG_plotEnrichAll           21.684  1.106  30.403
sesameQC_plotBetaByDesign    18.398  0.184  18.616
matchDesign                  17.454  0.284  18.850
inferSpecies                 17.077  0.658  21.007
compareMouseStrainReference  16.690  0.343  19.238
KYCG_annoProbes              16.633  0.339  20.323
diffRefSet                   16.030  0.300  18.511
compareReference             15.205  0.219  17.607
KYCG_plotMetaEnrichment      13.762  0.463  17.501
getRefSet                    12.982  0.427  15.596
sesameQC_plotBar             12.967  0.147  15.304
testEnrichmentSEA            12.767  0.132  16.369
KYCG_buildGeneDBs            11.943  0.367  14.695
visualizeGene                11.256  0.188  14.889
DMR                          10.997  0.379  13.755
inferStrain                  10.442  0.256  12.869
DML                           9.007  1.506  12.904
dyeBiasNL                     9.773  0.088  10.955
dbStats                       9.499  0.184  11.872
sdf_read_table                8.793  0.128  11.300
inferTissue                   8.457  0.135  10.757
estimateLeukocyte             7.664  0.431  10.290
KYCG_plotSetEnrichment        7.759  0.151  10.092
deidentify                    7.661  0.159   9.994
createUCSCtrack               7.042  0.112   9.321
openSesame                    6.886  0.184   9.247
probeSuccessRate              6.548  0.104   9.905
scrubSoft                     6.487  0.039   6.538
dyeBiasCorrMostBalanced       6.252  0.124   8.646
testEnrichment                6.213  0.148  10.794
reIdentify                    6.152  0.056   7.397
getMask                       5.702  0.275   9.241
sesameQC_rankStats            5.600  0.068   7.837
bisConversionControl          5.019  0.096   7.278
prepSesame                    4.807  0.071   5.969
checkLevels                   4.094  0.140   5.325
print.DMLSummary              3.754  0.144   6.059
totalIntensities              3.613  0.064   6.845
mapToMammal40                 3.534  0.088   5.796
dyeBiasCorr                   3.472  0.096   5.941
qualityMask                   3.297  0.068   5.518
meanIntensity                 3.255  0.100   5.510
summaryExtractTest            3.263  0.079  13.745
updateSigDF                   3.220  0.083   5.485
KYCG_getDBs                   3.191  0.099   5.444
KYCG_plotPointRange           2.790  0.072   5.545
* 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

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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, 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 
 22.809   2.204  27.197 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0000.0000.001
DML 9.007 1.50612.904
DMLpredict1.4730.0602.607
DMR10.997 0.37913.755
ELBAR23.137 0.46624.815
KYCG_annoProbes16.633 0.33920.323
KYCG_buildGeneDBs11.943 0.36714.695
KYCG_getDBs3.1910.0995.444
KYCG_listDBGroups0.0340.0000.035
KYCG_loadDBs000
KYCG_plotBar0.2350.0200.256
KYCG_plotDot0.4090.0520.462
KYCG_plotEnrichAll21.684 1.10630.403
KYCG_plotLollipop0.2300.0110.242
KYCG_plotManhattan1.7870.1081.898
KYCG_plotMeta26.035 0.49329.855
KYCG_plotMetaEnrichment13.762 0.46317.501
KYCG_plotPointRange2.7900.0725.545
KYCG_plotSetEnrichment 7.759 0.15110.092
KYCG_plotVolcano0.1920.0000.192
KYCG_plotWaterfall3.3670.1084.560
MValueToBetaValue0.0000.0000.001
SigDF0.3570.0161.445
addMask0.1200.0000.119
aggregateTestEnrichments4.1790.1204.307
betasCollapseToPfx0.0120.0040.016
bisConversionControl5.0190.0967.278
calcEffectSize1.4600.0672.616
checkLevels4.0940.1405.325
cnSegmentation0.3660.0241.464
compareMouseStrainReference16.690 0.34319.238
compareMouseTissueReference000
compareReference15.205 0.21917.607
controls2.3800.0604.588
createUCSCtrack7.0420.1129.321
dataFrame2sesameQC1.3460.0322.455
dbStats 9.499 0.18411.872
deidentify7.6610.1599.994
detectionPnegEcdf3.2730.0524.404
diffRefSet16.030 0.30018.511
dmContrasts2.4070.0393.531
dyeBiasCorr3.4720.0965.941
dyeBiasCorrMostBalanced6.2520.1248.646
dyeBiasL3.7520.1084.948
dyeBiasNL 9.773 0.08810.955
estimateLeukocyte 7.664 0.43110.290
formatVCF2.4220.1474.721
getAFTypeIbySumAlleles2.3020.1164.591
getAFs1.6700.1042.857
getBetas1.2280.0402.344
getMask5.7020.2759.241
getRefSet12.982 0.42715.596
imputeBetasMatrixByMean0.0030.0000.003
inferEthnicity1.9520.0643.096
inferInfiniumIChannel0.3550.0840.439
inferSex43.881 0.90249.188
inferSpecies17.077 0.65821.007
inferStrain10.442 0.25612.869
inferTissue 8.457 0.13510.757
initFileSet1.3610.0282.467
listAvailableMasks1.9330.0443.052
mLiftOver000
mapFileSet0.0370.0000.038
mapToMammal403.5340.0885.796
matchDesign17.454 0.28418.850
meanIntensity3.2550.1005.510
medianTotalIntensity1.2930.0672.432
noMasked2.5170.0403.641
noob3.4970.0643.567
openSesame6.8860.1849.247
openSesameToFile1.9140.0321.950
pOOBAH1.7030.0121.718
palgen0.0450.0000.049
parseGEOsignalMU3.7730.0364.888
predictAge2.4460.0444.143
predictAgeHorvath3530.0000.0000.001
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.5360.0000.537
prefixMaskButC0.1570.0000.157
prefixMaskButCG0.0710.0000.072
prepSesame4.8070.0715.969
prepSesameList0.0020.0000.002
print.DMLSummary3.7540.1446.059
print.fileSet1.3490.0362.459
probeID_designType000
probeSuccessRate6.5480.1049.905
qualityMask3.2970.0685.518
reIdentify6.1520.0567.397
readFileSet0.0560.0030.059
readIDATpair0.1620.0030.165
recommendedMaskNames000
resetMask0.4870.0161.575
scrub4.1970.1114.316
scrubSoft6.4870.0396.538
sdfPlatform0.3490.0161.431
sdf_read_table 8.793 0.12811.300
sdf_write_table2.1070.0643.291
searchIDATprefixes0.0000.0050.007
sesame-package2.2990.0413.432
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_get0.0010.0000.000
sesameAnno_readManifestTSV000
sesameData_getAnno000
sesameQC_calcStats29.761 0.13633.027
sesameQC_getStats2.3460.0042.353
sesameQC_plotBar12.967 0.14715.304
sesameQC_plotBetaByDesign18.398 0.18418.616
sesameQC_plotHeatSNPs25.914 0.13627.690
sesameQC_plotIntensVsBetas3.3810.0514.514
sesameQC_plotRedGrnQQ2.1030.0403.222
sesameQC_rankStats5.6000.0687.837
sesame_checkVersion0.0040.0000.004
sesamize0.0000.0000.001
setMask0.1470.0000.148
signalMU1.4650.0522.593
sliceFileSet0.0290.0050.033
summaryExtractTest 3.263 0.07913.745
testEnrichment 6.213 0.14810.794
testEnrichmentGene125.696 1.832149.358
testEnrichmentSEA12.767 0.13216.369
totalIntensities3.6130.0646.845
updateSigDF3.2200.0835.485
visualizeGene11.256 0.18814.889
visualizeProbes1.2510.0201.273
visualizeRegion0.4490.0000.449
visualizeSegments2.0750.0243.176