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This page was generated on 2024-02-21 12:53:53 -0500 (Wed, 21 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
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 1911/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.21.7  (landing page)
Wanding Zhou
Snapshot Date: 2024-02-20 14:10:09 -0500 (Tue, 20 Feb 2024)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: devel
git_last_commit: 2d5c2ab
git_last_commit_date: 2024-01-23 10:39:56 -0500 (Tue, 23 Jan 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

CHECK results for sesame on palomino3


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: 1.21.7
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sesame.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings sesame_1.21.7.tar.gz
StartedAt: 2024-02-21 08:11:56 -0500 (Wed, 21 Feb 2024)
EndedAt: 2024-02-21 08:33:17 -0500 (Wed, 21 Feb 2024)
EllapsedTime: 1281.7 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sesame.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings sesame_1.21.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck'
* using R Under development (unstable) (2024-01-14 r85805 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'sesame/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sesame' version '1.21.7'
* 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 whether package 'sesame' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 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          119.72   5.72  189.78
inferSex                     43.74   2.62   62.63
sesameQC_plotHeatSNPs        24.73   2.21   26.92
sesameQC_calcStats           24.49   2.28   26.77
KYCG_plotMeta                23.56   1.18   28.25
KYCG_plotEnrichAll           21.12   1.28   28.19
matchDesign                  17.14   1.03   18.19
inferSpecies                 15.90   1.30   23.51
convertTo                    15.63   0.94   41.27
sesameQC_plotBar             15.58   0.86   16.57
sdf_read_table               15.28   0.83   16.27
ELBAR                        14.36   1.53   18.20
KYCG_annoProbes              14.75   1.00   19.33
sesameQC_plotBetaByDesign    12.80   1.97   14.75
diffRefSet                   13.84   0.73   19.93
KYCG_buildGeneDBs            11.94   0.74   19.64
compareMouseStrainReference  11.69   0.66   13.97
DML                           9.42   2.33   50.08
testEnrichmentSEA            10.21   1.02   11.40
compareReference             10.36   0.72   11.16
getRefSet                    10.59   0.39   11.05
inferStrain                  10.00   0.91   11.06
visualizeGene                10.00   0.56   10.66
KYCG_plotMetaEnrichment       9.64   0.62   10.47
sdf_write_table               9.44   0.26    9.83
estimateLeukocyte             8.86   0.61   14.75
DMR                           8.08   0.44   10.39
dbStats                       7.03   0.93   15.12
inferTissue                   6.97   0.92    7.94
createUCSCtrack               7.15   0.37   10.39
openSesame                    5.96   0.79    7.54
dyeBiasCorrMostBalanced       6.26   0.41    6.73
dyeBiasNL                     6.24   0.39    6.64
testEnrichment                5.73   0.61    6.65
probeSuccessRate              5.68   0.56    6.30
KYCG_plotSetEnrichment        5.47   0.61    6.72
getMask                       5.49   0.48    7.17
bisConversionControl          5.08   0.25    8.96
deidentify                    4.93   0.33    5.44
scrubSoft                     4.39   0.78    5.17
prepSesame                    4.33   0.69    5.08
checkLevels                   3.17   0.24    6.25
updateSigDF                   2.66   0.39    5.06
* 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck/00check.log'
for details.



Installation output

sesame.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 1 ]
> 
> proc.time()
   user  system elapsed 
  21.56    2.32   24.04 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML 9.42 2.3350.08
DMLpredict1.110.151.31
DMR 8.08 0.4410.39
ELBAR14.36 1.5318.20
KYCG_annoProbes14.75 1.0019.33
KYCG_buildGeneDBs11.94 0.7419.64
KYCG_getDBs2.840.323.75
KYCG_listDBGroups0.030.020.05
KYCG_loadDBs000
KYCG_plotBar0.190.010.20
KYCG_plotDot0.270.020.28
KYCG_plotEnrichAll21.12 1.2828.19
KYCG_plotLollipop0.160.000.16
KYCG_plotManhattan1.390.061.43
KYCG_plotMeta23.56 1.1828.25
KYCG_plotMetaEnrichment 9.64 0.6210.47
KYCG_plotPointRange3.300.273.58
KYCG_plotSetEnrichment5.470.616.72
KYCG_plotVolcano0.140.010.16
KYCG_plotWaterfall2.530.333.18
MValueToBetaValue000
SigDF0.270.060.35
addMask0.070.000.08
aggregateTestEnrichments1.820.141.95
betasCollapseToPfx0.010.000.01
bisConversionControl5.080.258.96
calcEffectSize1.140.111.28
checkLevels3.170.246.25
cnSegmentation0.250.070.34
compareMouseStrainReference11.69 0.6613.97
compareMouseTissueReference000
compareReference10.36 0.7211.16
controls1.770.332.11
convertTo15.63 0.9441.27
createUCSCtrack 7.15 0.3710.39
dataFrame2sesameQC1.080.161.59
dbStats 7.03 0.9315.12
deidentify4.930.335.44
detectionPnegEcdf3.300.163.49
diffRefSet13.84 0.7319.93
dmContrasts2.110.212.33
dyeBiasCorr2.520.322.89
dyeBiasCorrMostBalanced6.260.416.73
dyeBiasL2.640.142.81
dyeBiasNL6.240.396.64
estimateLeukocyte 8.86 0.6114.75
formatVCF2.180.402.73
getAFTypeIbySumAlleles2.080.332.68
getAFs1.110.171.31
getBetas0.810.130.95
getMask5.490.487.17
getRefSet10.59 0.3911.05
imputeTo2.020.252.38
inferEthnicity1.920.252.18
inferInfiniumIChannel0.560.380.94
inferSex43.74 2.6262.63
inferSpecies15.90 1.3023.51
inferStrain10.00 0.9111.06
inferTissue6.970.927.94
initFileSet1.360.191.56
liftOver000
listAvailableMasks1.770.101.89
mapFileSet0.030.000.05
mapToMammal403.480.524.22
matchDesign17.14 1.0318.19
meanIntensity2.660.473.15
medianTotalIntensity0.970.201.19
noMasked1.970.252.24
noob3.180.433.61
openSesame5.960.797.54
openSesameToFile1.890.112.00
pOOBAH1.610.081.69
palgen0.040.020.09
parseGEOsignalMU3.190.483.66
predictAge2.340.232.72
predictAgeHorvath353000
predictAgeSkinBlood000
predictMouseAgeInMonth000
prefixMask0.540.000.53
prefixMaskButC0.140.000.14
prefixMaskButCG0.060.000.06
prepSesame4.330.695.08
prepSesameList000
print.DMLSummary3.010.413.56
print.fileSet1.310.311.64
probeID_designType000
probeSuccessRate5.680.566.30
qualityMask2.640.282.97
reIdentify4.420.144.70
readFileSet0.060.000.07
readIDATpair0.130.020.14
recommendedMaskNames000
resetMask0.370.060.57
scrub4.240.614.85
scrubSoft4.390.785.17
sdfPlatform0.390.080.61
sdf_read_table15.28 0.8316.27
sdf_write_table9.440.269.83
searchIDATprefixes000
sesame-package1.960.172.17
sesameAnno_buildAddressFile000
sesameAnno_buildManifestGRanges000
sesameAnno_download000
sesameAnno_get000
sesameAnno_readManifestTSV000
sesameData_getAnno000
sesameQC_calcStats24.49 2.2826.77
sesameQC_getStats3.330.143.46
sesameQC_plotBar15.58 0.8616.57
sesameQC_plotBetaByDesign12.80 1.9714.75
sesameQC_plotHeatSNPs24.73 2.2126.92
sesameQC_plotIntensVsBetas2.300.452.85
sesameQC_plotRedGrnQQ1.390.191.58
sesameQC_rankStats3.620.614.29
sesame_checkVersion0.000.000.05
sesamize000
setMask0.090.010.11
signalMU0.860.141.03
sliceFileSet0.050.000.06
summaryExtractTest3.220.313.58
testEnrichment5.730.616.65
testEnrichmentGene119.72 5.72189.78
testEnrichmentSEA10.21 1.0211.40
totalIntensities3.040.303.37
updateSigDF2.660.395.06
visualizeGene10.00 0.5610.66
visualizeProbes0.970.030.98
visualizeRegion3.840.083.93
visualizeSegments2.060.222.25