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This page was generated on 2023-10-16 11:37:32 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1897/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.18.4  (landing page)
Wanding Zhou
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_17
git_last_commit: eba556b
git_last_commit_date: 2023-05-04 15:22:47 -0400 (Thu, 04 May 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for sesame on merida1


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: 1.18.4
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_1.18.4.tar.gz
StartedAt: 2023-10-16 07:02:36 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 07:36:01 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 2004.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: sesame.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_1.18.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/sesame.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.18.4’
* 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 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘BiocManager’
* 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          173.361  6.526 236.118
sesameQC_calcStats           37.981  1.761  48.613
KYCG_plotMeta                33.412  1.046  44.335
sesameQC_plotHeatSNPs        32.513  1.578  43.312
KYCG_plotEnrichAll           30.465  1.315  42.394
compareMouseStrainReference  29.723  0.540  38.934
compareReference             26.657  0.814  35.554
inferSpecies                 25.258  1.095  33.831
ELBAR                        22.487  2.761  33.658
matchDesign                  23.871  1.162  33.146
diffRefSet                   22.882  0.716  30.375
KYCG_annoProbes              21.978  0.996  30.883
sesameQC_plotBar             19.909  0.484  26.432
KYCG_plotMetaEnrichment      18.611  0.644  25.561
testEnrichmentSEA            18.267  0.950  24.342
getRefSet                    18.498  0.670  25.096
sesameQC_plotBetaByDesign    17.744  1.048  23.893
inferTissue                  16.302  1.479  23.587
DML                          15.681  1.656  23.544
KYCG_buildGeneDBs            16.132  0.588  22.851
sdf_read_table               15.404  0.611  20.553
visualizeGene                15.469  0.543  20.231
DMR                          15.552  0.427  21.475
getSexInfo                   14.561  0.606  19.538
deidentify                   13.706  0.460  18.901
inferStrain                  12.707  0.875  17.590
reIdentify                   12.107  0.344  17.342
estimateLeukocyte             9.939  0.546  14.246
dbStats                       9.333  0.706  13.379
KYCG_plotSetEnrichment        9.390  0.524  12.912
dyeBiasNL                     9.201  0.554  12.324
dyeBiasCorrMostBalanced       9.290  0.320  12.605
openSesame                    8.730  0.774  12.438
createUCSCtrack               9.035  0.335  12.903
probeSuccessRate              8.490  0.672  12.209
testEnrichment                8.068  0.558  12.218
inferSex                      8.027  0.470  10.982
getMask                       7.583  0.518  10.991
bisConversionControl          7.487  0.295  10.154
visualizeProbes               7.512  0.238   9.618
prepSesame                    6.246  0.427   8.585
sdf_write_table               5.733  0.324   7.543
scrubSoft                     5.365  0.644   7.568
sesameQC_rankStats            5.678  0.303   8.139
inferSexKaryotypes            5.361  0.260   7.238
formatVCF                     5.237  0.374   7.368
KYCG_plotWaterfall            5.002  0.206   7.060
totalIntensities              4.770  0.386   6.514
KYCG_getDBs                   4.774  0.340   6.883
mapToMammal40                 4.700  0.384   7.100
print.DMLSummary              3.949  1.027   6.437
updateSigDF                   4.625  0.302   6.400
detectionPnegEcdf             4.714  0.159   6.704
parseGEOsignalMU              4.651  0.197   6.078
checkLevels                   4.407  0.428   6.325
dyeBiasCorr                   4.326  0.264   6.146
meanIntensity                 4.183  0.314   5.873
summaryExtractTest            3.728  0.692   6.136
qualityMask                   3.741  0.469   6.334
scrub                         3.844  0.297   5.488
sesameQC_getStats             3.933  0.188   5.083
sesame-package                3.643  0.458   5.063
KYCG_plotPointRange           3.821  0.212   5.218
inferEthnicity                3.675  0.245   5.244
noMasked                      3.271  0.467   5.095
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/sesame.Rcheck/00check.log’
for details.



Installation output

sesame.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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, sort, 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 
 34.235   3.281  46.803 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0000.0010.001
DML15.681 1.65623.544
DMLpredict2.2050.1643.418
DMR15.552 0.42721.475
ELBAR22.487 2.76133.658
KYCG_annoProbes21.978 0.99630.883
KYCG_buildGeneDBs16.132 0.58822.851
KYCG_getDBs4.7740.3406.883
KYCG_listDBGroups0.0550.0010.071
KYCG_loadDBs0.0000.0010.001
KYCG_plotBar0.3960.0130.507
KYCG_plotDot0.6020.0360.815
KYCG_plotEnrichAll30.465 1.31542.394
KYCG_plotLollipop0.3700.0150.491
KYCG_plotManhattan1.5130.2502.269
KYCG_plotMeta33.412 1.04644.335
KYCG_plotMetaEnrichment18.611 0.64425.561
KYCG_plotPointRange3.8210.2125.218
KYCG_plotSetEnrichment 9.390 0.52412.912
KYCG_plotVolcano0.3760.0060.521
KYCG_plotWaterfall5.0020.2067.060
MValueToBetaValue0.0000.0000.001
SigDF0.4930.0650.831
addMask0.1580.0010.207
aggregateTestEnrichments3.2780.0894.263
betasCollapseToPfx0.0040.0010.004
bisConversionControl 7.487 0.29510.154
calcEffectSize1.9680.1442.798
checkLevels4.4070.4286.325
cnSegmentation0.4860.0790.851
compareMouseStrainReference29.723 0.54038.934
compareMouseTissueReference0.0010.0010.001
compareReference26.657 0.81435.554
controls3.3020.2444.928
createUCSCtrack 9.035 0.33512.903
dataFrame2sesameQC2.4360.2193.566
dbStats 9.333 0.70613.379
deidentify13.706 0.46018.901
detectionPnegEcdf4.7140.1596.704
diffRefSet22.882 0.71630.375
dmContrasts2.9630.3354.348
dyeBiasCorr4.3260.2646.146
dyeBiasCorrMostBalanced 9.290 0.32012.605
dyeBiasL3.6030.1604.841
dyeBiasNL 9.201 0.55412.324
estimateLeukocyte 9.939 0.54614.246
formatVCF5.2370.3747.368
getAFTypeIbySumAlleles2.4650.2213.614
getAFs1.6370.1162.312
getBetas1.3380.1251.929
getMask 7.583 0.51810.991
getRefSet18.498 0.67025.096
getSexInfo14.561 0.60619.538
imputeTo2.8130.2344.005
inferEthnicity3.6750.2455.244
inferInfiniumIChannel1.0151.4763.171
inferSex 8.027 0.47010.982
inferSexKaryotypes5.3610.2607.238
inferSpecies25.258 1.09533.831
inferStrain12.707 0.87517.590
inferTissue16.302 1.47923.587
initFileSet1.9520.2812.885
listAvailableMasks2.7350.1573.848
mapFileSet0.0610.0060.091
mapToMammal404.7000.3847.100
matchDesign23.871 1.16233.146
meanIntensity4.1830.3145.873
medianTotalIntensity1.3910.0782.082
noMasked3.2710.4675.095
noob3.3050.0384.450
openSesame 8.730 0.77412.438
openSesameToFile2.8500.2603.938
pOOBAH2.3670.0072.950
palgen0.0690.0120.096
parseGEOsignalMU4.6510.1976.078
predictAge3.6710.1624.899
predictAgeHorvath3530.0010.0000.000
predictAgeSkinBlood0.0010.0000.001
predictMouseAgeInMonth0.0000.0010.001
prefixMask1.1680.0051.488
prefixMaskButC0.3290.0020.415
prefixMaskButCG0.1300.0020.199
prepSesame6.2460.4278.585
prepSesameList0.0020.0020.004
print.DMLSummary3.9491.0276.437
print.fileSet1.9110.2302.834
probeID_designType0.0000.0000.001
probeSuccessRate 8.490 0.67212.209
qualityMask3.7410.4696.334
reIdentify12.107 0.34417.342
readFileSet0.0910.0100.195
readIDATpair0.2180.0050.260
recommendedMaskNames0.0000.0010.002
resetMask0.6500.0661.081
scrub3.8440.2975.488
scrubSoft5.3650.6447.568
sdfPlatform0.4830.0790.826
sdf_read_table15.404 0.61120.553
sdf_write_table5.7330.3247.543
searchIDATprefixes0.0060.0040.011
sesame-package3.6430.4585.063
sesameAnno_download0.0000.0010.001
sesameAnno_get0.0000.0010.003
sesameData_getAnno0.0010.0000.001
sesameQC_calcStats37.981 1.76148.613
sesameQC_getStats3.9330.1885.083
sesameQC_plotBar19.909 0.48426.432
sesameQC_plotBetaByDesign17.744 1.04823.893
sesameQC_plotHeatSNPs32.513 1.57843.312
sesameQC_plotIntensVsBetas3.2390.2824.971
sesameQC_plotRedGrnQQ2.2350.2623.325
sesameQC_rankStats5.6780.3038.139
sesame_checkVersion0.0060.0020.009
setMask0.1840.0010.232
signalMU1.5730.3002.497
sliceFileSet0.0600.0060.083
summaryExtractTest3.7280.6926.136
testEnrichment 8.068 0.55812.218
testEnrichmentGene173.361 6.526236.118
testEnrichmentSEA18.267 0.95024.342
totalIntensities4.7700.3866.514
updateSigDF4.6250.3026.400
visualizeGene15.469 0.54320.231
visualizeProbes7.5120.2389.618
visualizeRegion0.7260.0050.905
visualizeSegments2.2290.6843.670