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This page was generated on 2024-03-28 11:41:19 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1929/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.21.15  (landing page)
Wanding Zhou
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: devel
git_last_commit: 1a92c64
git_last_commit_date: 2024-03-20 08:08:36 -0400 (Wed, 20 Mar 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  

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: 1.21.15
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings sesame_1.21.15.tar.gz
StartedAt: 2024-03-28 09:35:46 -0000 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 09:57:01 -0000 (Thu, 28 Mar 2024)
EllapsedTime: 1275.3 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings sesame_1.21.15.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* 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 ‘1.21.15’
* 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          123.630  1.817 147.410
inferSex                     43.134  0.434  47.988
sesameQC_calcStats           32.307  0.471  33.915
sesameQC_plotHeatSNPs        27.841  0.175  29.145
KYCG_plotMeta                26.527  0.267  30.056
ELBAR                        23.754  0.319  25.208
KYCG_plotEnrichAll           21.712  0.395  29.710
matchDesign                  20.809  0.243  22.176
inferSpecies                 19.794  0.522  23.571
sesameQC_plotBetaByDesign    19.561  0.148  19.747
KYCG_annoProbes              16.391  0.404  20.211
compareMouseStrainReference  16.360  0.104  18.686
diffRefSet                   16.243  0.219  18.649
compareReference             14.863  0.244  17.284
KYCG_plotMetaEnrichment      13.618  0.251  17.129
sesameQC_plotBar             13.045  0.216  15.426
getRefSet                    12.915  0.163  15.241
testEnrichmentSEA            12.673  0.131  16.255
KYCG_buildGeneDBs            11.847  0.355  14.499
DMR                          10.815  0.358  13.363
visualizeGene                10.785  0.152  14.175
inferStrain                  10.360  0.220  12.735
DML                           8.887  0.461  11.649
estimateLeukocyte             9.124  0.163  11.471
sdf_read_table                8.763  0.200  11.221
inferTissue                   8.329  0.263  10.761
dbStats                       8.281  0.140  10.597
KYCG_plotSetEnrichment        7.777  0.155  10.957
deidentify                    7.691  0.068   9.927
dyeBiasNL                     7.593  0.064   8.742
dyeBiasCorrMostBalanced       7.332  0.164   9.647
scrubSoft                     6.680  0.115   6.810
openSesame                    6.363  0.387   8.946
createUCSCtrack               6.573  0.095   8.840
reIdentify                    6.458  0.187   7.722
probeSuccessRate              6.395  0.204   9.818
testEnrichment                6.204  0.187   9.639
sesameQC_rankStats            5.652  0.088   8.001
getMask                       5.554  0.096   8.866
prepSesame                    5.030  0.316   6.422
bisConversionControl          4.984  0.097   7.247
checkLevels                   4.034  0.075   5.186
parseGEOsignalMU              3.780  0.207   5.067
print.DMLSummary              3.439  0.347   5.962
dyeBiasCorr                   3.557  0.072   5.882
totalIntensities              3.505  0.064   5.725
mapToMammal40                 3.283  0.104   5.550
meanIntensity                 3.322  0.048   5.571
updateSigDF                   3.286  0.084   5.542
KYCG_getDBs                   3.216  0.124   5.587
summaryExtractTest            3.110  0.092   5.355
qualityMask                   2.730  0.152   5.044
* 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-4.4-devel-2024.03.20/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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 Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
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 
 22.541   0.724  25.427 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML 8.887 0.46111.649
DMLpredict1.5170.0882.787
DMR10.815 0.35813.363
ELBAR23.754 0.31925.208
KYCG_annoProbes16.391 0.40420.211
KYCG_buildGeneDBs11.847 0.35514.499
KYCG_getDBs3.2160.1245.587
KYCG_listDBGroups0.0360.0000.036
KYCG_loadDBs000
KYCG_plotBar0.240.000.24
KYCG_plotDot1.0880.0161.106
KYCG_plotEnrichAll21.712 0.39529.710
KYCG_plotLollipop0.2210.0000.221
KYCG_plotManhattan1.5240.0601.587
KYCG_plotMeta26.527 0.26730.056
KYCG_plotMetaEnrichment13.618 0.25117.129
KYCG_plotPointRange2.7000.0403.811
KYCG_plotSetEnrichment 7.777 0.15510.957
KYCG_plotVolcano0.1990.0040.204
KYCG_plotWaterfall3.2160.0684.459
MValueToBetaValue000
SigDF0.3860.0041.676
addMask0.1120.0040.116
aggregateTestEnrichments2.3450.0202.371
betasCollapseToPfx0.0140.0030.016
bisConversionControl4.9840.0977.247
calcEffectSize1.5850.0642.716
checkLevels4.0340.0755.186
cnSegmentation0.3780.0201.469
compareMouseStrainReference16.360 0.10418.686
compareMouseTissueReference000
compareReference14.863 0.24417.284
controls2.3020.0564.522
createUCSCtrack6.5730.0958.840
dataFrame2sesameQC1.6040.0362.720
dbStats 8.281 0.14010.597
deidentify7.6910.0689.927
detectionPnegEcdf3.1330.0604.269
diffRefSet16.243 0.21918.649
dmContrasts2.4250.0363.549
dyeBiasCorr3.5570.0725.882
dyeBiasCorrMostBalanced7.3320.1649.647
dyeBiasL3.5360.0404.660
dyeBiasNL7.5930.0648.742
estimateLeukocyte 9.124 0.16311.471
formatVCF2.3860.0644.619
getAFTypeIbySumAlleles2.2830.0724.512
getAFs1.6100.0402.827
getBetas1.1760.0202.271
getMask5.5540.0968.866
getRefSet12.915 0.16315.241
imputeBetasMatrixByMean0.0020.0000.002
inferEthnicity1.9890.0323.097
inferInfiniumIChannel0.3310.0800.412
inferSex43.134 0.43447.988
inferSpecies19.794 0.52223.571
inferStrain10.360 0.22012.735
inferTissue 8.329 0.26310.761
initFileSet1.4000.0362.502
listAvailableMasks1.9650.0523.088
mLiftOver0.0010.0000.000
mapFileSet0.0340.0040.038
mapToMammal403.2830.1045.550
matchDesign20.809 0.24322.176
meanIntensity3.3220.0485.571
medianTotalIntensity1.3140.0322.493
noMasked2.260.103.51
noob3.7500.0963.853
openSesame6.3630.3878.946
openSesameToFile2.0110.0602.077
pOOBAH1.7160.0391.757
palgen0.0500.0040.055
parseGEOsignalMU3.7800.2075.067
predictAge2.6010.1153.795
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.5260.0040.531
prefixMaskButC0.1530.0000.154
prefixMaskButCG0.0710.0000.071
prepSesame5.0300.3166.422
prepSesameList0.0020.0000.002
print.DMLSummary3.4390.3475.962
print.fileSet1.2820.0462.398
probeID_designType0.0010.0000.000
probeSuccessRate6.3950.2049.818
qualityMask2.7300.1525.044
reIdentify6.4580.1877.722
readFileSet0.0550.0000.054
readIDATpair0.1530.0040.157
recommendedMaskNames000
resetMask0.4700.0521.590
scrub4.3880.1484.546
scrubSoft6.6800.1156.810
sdfPlatform0.4630.0311.590
sdf_read_table 8.763 0.20011.221
sdf_write_table2.1850.0643.366
searchIDATprefixes0.0020.0030.007
sesame-package3.1130.1484.342
sesameAnno_buildAddressFile0.0000.0000.001
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_get0.0000.0000.001
sesameAnno_readManifestTSV000
sesameData_getAnno000
sesameQC_calcStats32.307 0.47133.915
sesameQC_getStats2.3730.0352.414
sesameQC_plotBar13.045 0.21615.426
sesameQC_plotBetaByDesign19.561 0.14819.747
sesameQC_plotHeatSNPs27.841 0.17529.145
sesameQC_plotIntensVsBetas3.6600.0324.771
sesameQC_plotRedGrnQQ1.7540.0362.858
sesameQC_rankStats5.6520.0888.001
sesame_checkVersion0.0050.0000.004
sesamize000
setMask0.4010.0000.402
signalMU1.4910.0202.594
sliceFileSet0.040.000.04
summaryExtractTest3.1100.0925.355
testEnrichment6.2040.1879.639
testEnrichmentGene123.630 1.817147.410
testEnrichmentSEA12.673 0.13116.255
totalIntensities3.5050.0645.725
updateSigDF3.2860.0845.542
visualizeGene10.785 0.15214.175
visualizeProbes1.2350.0031.251
visualizeRegion4.0380.0284.078
visualizeSegments1.9010.0202.999