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This page was generated on 2024-05-04 11:39:58 -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 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: 1.22.0
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_1.22.0.tar.gz
StartedAt: 2024-05-04 00:54:16 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 01:12:18 -0400 (Sat, 04 May 2024)
EllapsedTime: 1081.9 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_1.22.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    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 ‘1.22.0’
* 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 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          126.128  5.678 135.130
inferSex                     41.734  2.005  44.363
sesameQC_calcStats           25.784  2.040  28.155
KYCG_plotMeta                25.945  1.208  27.812
sesameQC_plotHeatSNPs        23.136  2.121  25.585
KYCG_plotEnrichAll           21.096  1.162  22.864
ELBAR                        18.055  3.230  21.634
inferSpecies                 18.139  0.832  19.297
KYCG_annoProbes              15.426  1.055  16.870
diffRefSet                   15.680  0.796  16.823
sesameQC_plotBar             14.708  0.709  15.664
compareMouseStrainReference  14.094  0.441  14.737
KYCG_plotMetaEnrichment      13.638  0.708  14.661
getRefSet                    12.900  0.677  13.885
sesameQC_plotBetaByDesign    11.543  1.488  13.167
compareReference             12.281  0.723  13.248
matchDesign                  12.119  0.635  12.909
KYCG_buildGeneDBs            11.806  0.569  12.702
visualizeGene                11.789  0.559  12.631
testEnrichmentSEA            11.205  0.842  12.384
DML                           9.477  1.362  11.468
sdf_read_table               10.178  0.585  10.993
DMR                           9.723  0.357  10.298
inferStrain                   9.250  0.764  10.240
inferTissue                   8.148  1.443   9.930
estimateLeukocyte             8.699  0.632   9.523
dbStats                       8.120  0.650   8.958
dyeBiasNL                     6.806  0.550   7.480
createUCSCtrack               6.941  0.376   7.481
KYCG_plotSetEnrichment        6.412  0.545   7.227
testEnrichment                6.168  0.746   7.256
dyeBiasCorrMostBalanced       6.481  0.334   7.024
probeSuccessRate              6.267  0.397   6.996
openSesame                    5.893  0.764   6.955
deidentify                    6.211  0.401   6.783
getMask                       5.546  0.434   6.454
bisConversionControl          5.562  0.317   6.029
reIdentify                    5.100  0.186   5.391
prepSesame                    4.560  0.554   5.239
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
 23.995   2.091  26.919 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0000.0010.000
DML 9.477 1.36211.468
DMLpredict1.4630.1321.664
DMR 9.723 0.35710.298
ELBAR18.055 3.23021.634
KYCG_annoProbes15.426 1.05516.870
KYCG_buildGeneDBs11.806 0.56912.702
KYCG_getDBs3.0890.2763.508
KYCG_listDBGroups0.0320.0020.034
KYCG_loadDBs0.0010.0000.001
KYCG_plotBar0.2240.0120.238
KYCG_plotDot0.6700.0410.718
KYCG_plotEnrichAll21.096 1.16222.864
KYCG_plotLollipop0.1850.0060.192
KYCG_plotManhattan1.3210.1581.488
KYCG_plotMeta25.945 1.20827.812
KYCG_plotMetaEnrichment13.638 0.70814.661
KYCG_plotPointRange2.8090.2553.138
KYCG_plotSetEnrichment6.4120.5457.227
KYCG_plotVolcano0.1840.0070.193
KYCG_plotWaterfall3.1670.2413.500
MValueToBetaValue0.0000.0000.001
SigDF0.3500.0500.452
addMask0.1190.0010.120
aggregateTestEnrichments2.4990.1332.650
betasCollapseToPfx0.0130.0010.014
bisConversionControl5.5620.3176.029
calcEffectSize1.6940.1351.894
checkLevels4.1770.4484.717
cnSegmentation0.3320.0800.493
compareMouseStrainReference14.094 0.44114.737
compareMouseTissueReference0.0000.0010.000
compareReference12.281 0.72313.248
controls2.2670.2322.624
createUCSCtrack6.9410.3767.481
dataFrame2sesameQC1.3070.1641.539
dbStats8.1200.6508.958
deidentify6.2110.4016.783
detectionPnegEcdf3.1140.1723.616
diffRefSet15.680 0.79616.823
dmContrasts2.1650.2222.455
dyeBiasCorr3.1550.2623.676
dyeBiasCorrMostBalanced6.4810.3347.024
dyeBiasL3.1510.1803.414
dyeBiasNL6.8060.5507.480
estimateLeukocyte8.6990.6329.523
formatVCF2.2980.2832.726
getAFTypeIbySumAlleles2.1070.2272.472
getAFs1.3610.1181.545
getBetas1.0210.1191.196
getMask5.5460.4346.454
getRefSet12.900 0.67713.885
imputeBetasMatrixByMean0.0010.0010.002
inferEthnicity1.9680.2142.281
inferInfiniumIChannel0.4360.5420.997
inferSex41.734 2.00544.363
inferSpecies18.139 0.83219.297
inferStrain 9.250 0.76410.240
inferTissue8.1481.4439.930
initFileSet1.3750.2761.721
listAvailableMasks2.0820.1692.331
mLiftOver0.0000.0020.002
mapFileSet0.0390.0050.046
mapToMammal403.6890.3844.459
matchDesign12.119 0.63512.909
meanIntensity3.1280.5203.810
medianTotalIntensity1.0410.0561.154
noMasked1.9940.0632.123
noob2.4540.5183.002
openSesame5.8930.7646.955
openSesameToFile1.6150.0351.669
pOOBAH1.5840.0181.618
palgen0.0490.0110.066
parseGEOsignalMU3.3980.4743.987
predictAge2.5160.1482.782
predictAgeHorvath3530.0000.0010.000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.8150.0070.832
prefixMaskButC0.2010.0010.203
prefixMaskButCG0.0760.0010.077
prepSesame4.5600.5545.239
prepSesameList0.0110.0010.012
print.DMLSummary3.1590.6213.936
print.fileSet1.3410.2281.644
probeID_designType0.0000.0000.001
probeSuccessRate6.2670.3976.996
qualityMask3.1930.4263.772
reIdentify5.1000.1865.391
readFileSet0.0590.0040.066
readIDATpair0.1740.0040.181
recommendedMaskNames0.0000.0000.001
resetMask0.4710.0590.689
scrub2.5760.5043.131
scrubSoft3.6000.4934.134
sdfPlatform0.4740.4891.032
sdf_read_table10.178 0.58510.993
sdf_write_table2.9080.2053.210
searchIDATprefixes0.0050.0020.007
sesame-package3.0140.2933.433
sesameAnno_buildAddressFile0.0000.0010.001
sesameAnno_buildManifestGRanges0.0000.0010.000
sesameAnno_download0.0000.0010.001
sesameAnno_get0.0010.0000.001
sesameAnno_readManifestTSV000
sesameData_getAnno000
sesameQC_calcStats25.784 2.04028.155
sesameQC_getStats2.3180.0222.359
sesameQC_plotBar14.708 0.70915.664
sesameQC_plotBetaByDesign11.543 1.48813.167
sesameQC_plotHeatSNPs23.136 2.12125.585
sesameQC_plotIntensVsBetas2.2280.3292.636
sesameQC_plotRedGrnQQ1.2500.1521.471
sesameQC_rankStats4.2210.5474.931
sesame_checkVersion0.0040.0020.005
sesamize000
setMask0.1410.0010.143
signalMU0.9400.0791.085
sliceFileSet0.0440.0030.048
summaryExtractTest2.890.733.75
testEnrichment6.1680.7467.256
testEnrichmentGene126.128 5.678135.130
testEnrichmentSEA11.205 0.84212.384
totalIntensities3.6030.3324.073
updateSigDF3.2640.3053.741
visualizeGene11.789 0.55912.631
visualizeProbes1.1430.0101.162
visualizeRegion3.9920.3194.349
visualizeSegments1.8490.7012.625