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This page was generated on 2022-07-01 12:07:16 -0400 (Fri, 01 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for sesame on palomino3


To the developers/maintainers of the sesame package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1823/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.14.2  (landing page)
Wanding Zhou
Snapshot Date: 2022-06-30 13:55:04 -0400 (Thu, 30 Jun 2022)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_15
git_last_commit: 67b0bdb
git_last_commit_date: 2022-05-17 20:40:09 -0400 (Tue, 17 May 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: sesame
Version: 1.14.2
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sesame.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings sesame_1.14.2.tar.gz
StartedAt: 2022-07-01 03:37:44 -0400 (Fri, 01 Jul 2022)
EndedAt: 2022-07-01 03:54:37 -0400 (Fri, 01 Jul 2022)
EllapsedTime: 1013.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: sesame.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sesame.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings sesame_1.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/sesame.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'sesame/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sesame' version '1.14.2'
* 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 ... WARNING
Found the following significant warnings:
  Warning: package 'dbplyr' was built under R version 4.2.1
See 'F:/biocbuild/bbs-3.15-bioc/meat/sesame.Rcheck/00install.out' for details.
* 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 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
sesameQC_calcStats          29.49   1.00   30.52
KYCG_plotEnrichAll          24.97   1.27   36.36
DMR                         25.26   0.61   26.20
sesameQC_plotHeatSNPs       24.61   0.95   25.61
DML                         19.54   1.70   41.57
matchDesign                 19.27   0.77   20.11
inferSpecies                18.11   0.97   26.03
sesameQC_plotBetaByDesign   14.84   0.81   15.65
dyeBiasCorrMostBalanced     14.42   0.69   27.41
compareMouseStrainReference 13.75   0.59   16.95
sesameQC_plotBar            13.25   0.64   27.18
KYCG_plotMeta               12.89   0.78   19.01
diffRefSet                  12.15   0.48   20.22
sdf_read_table              11.61   0.40   12.07
getSexInfo                  10.93   0.64   11.73
KYCG_plotMetaEnrichment     10.97   0.56   11.77
KYCG_buildGeneDBs           10.47   0.44   19.42
KYCG_annoProbes             10.30   0.55   12.93
probeSuccessRate            10.18   0.61   11.01
compareMouseTissueReference 10.22   0.50   10.83
dyeBiasCorr                  9.81   0.64   10.62
prepSesame                   9.58   0.61   10.33
testEnrichmentGSEA           9.40   0.61   10.96
inferStrain                  9.19   0.72    9.97
getRefSet                    9.57   0.28   10.02
visualizeGene                8.75   0.40    9.27
testEnrichment               7.83   0.63    8.63
sdf_write_table              8.14   0.20    8.39
dbStats                      7.48   0.59   16.38
estimateLeukocyte            7.47   0.50   16.88
controls                     7.54   0.36    8.22
inferTissue                  7.09   0.47    7.65
detectionIB                  6.45   0.39    6.89
formatVCF                    6.20   0.47    7.43
mapToMammal40                6.08   0.56    7.27
detectionPnegEcdf            6.24   0.22    6.53
scrubSoft                    5.86   0.39    6.25
deidentify                   5.55   0.30    6.01
createUCSCtrack              5.49   0.25    8.69
predictAgeHorvath353         5.05   0.47    5.73
openSesame                   4.94   0.51    6.72
dyeBiasNL                    5.11   0.30    5.42
inferSex                     5.01   0.32    5.39
scrub                        5.07   0.24    5.30
noMasked                     4.89   0.35    5.33
bisConversionControl         4.37   0.22    9.32
updateSigDF                  2.65   0.27    5.08
checkLevels                  2.68   0.22    5.85
* 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
  'F:/biocbuild/bbs-3.15-bioc/meat/sesame.Rcheck/00check.log'
for details.



Installation output

sesame.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'sesame' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
package 'dbplyr' was built under R version 4.2.1 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: package 'dbplyr' was built under R version 4.2.1
** testing if installed package can be loaded from final location
Warning: package 'dbplyr' was built under R version 4.2.1
** testing if installed package keeps a record of temporary installation path
* DONE (sesame)

Tests output

sesame.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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.
----------------------------------------------------------

Warning message:
package 'dbplyr' was built under R version 4.2.1 
> 
> test_check("sesame")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  24.81    2.31   27.42 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML19.54 1.7041.57
DMR25.26 0.6126.20
KYCG_annoProbes10.30 0.5512.93
KYCG_buildGeneDBs10.47 0.4419.42
KYCG_getDBs2.030.233.06
KYCG_listDBGroups0.030.000.03
KYCG_plotBar0.310.000.31
KYCG_plotDot0.240.000.24
KYCG_plotEnrichAll24.97 1.2736.36
KYCG_plotLollipop0.140.000.14
KYCG_plotManhattan1.150.031.19
KYCG_plotMeta12.89 0.7819.01
KYCG_plotMetaEnrichment10.97 0.5611.77
KYCG_plotPointRange2.490.222.73
KYCG_plotVolcano0.260.000.27
KYCG_plotWaterfall3.550.194.28
MValueToBetaValue000
SigDF0.200.080.30
addMask0.060.000.06
aggregateTestEnrichments1.190.121.32
bisConversionControl4.370.229.32
checkLevels2.680.225.85
cnSegmentation0.260.020.31
compareMouseStrainReference13.75 0.5916.95
compareMouseTissueReference10.22 0.5010.83
controls7.540.368.22
createUCSCtrack5.490.258.69
dataFrame2sesameQC0.890.161.19
dbStats 7.48 0.5916.38
deidentify5.550.306.01
detectionIB6.450.396.89
detectionPnegEcdf6.240.226.53
diffRefSet12.15 0.4820.22
dmContrasts2.130.142.32
dyeBiasCorr 9.81 0.6410.62
dyeBiasCorrMostBalanced14.42 0.6927.41
dyeBiasL2.520.092.65
dyeBiasNL5.110.305.42
estimateLeukocyte 7.47 0.5016.88
formatVCF6.200.477.43
getAFTypeIbySumAlleles1.400.252.05
getAFs1.090.091.22
getBetas0.500.000.55
getRefSet 9.57 0.2810.02
getSexInfo10.93 0.6411.73
inferEthnicity3.930.164.16
inferInfiniumIChannel0.660.421.08
inferSex5.010.325.39
inferSexKaryotypes3.330.153.52
inferSpecies18.11 0.9726.03
inferStrain9.190.729.97
inferTissue7.090.477.65
initFileSet0.900.081.03
listAvailableMasks1.410.182.42
mapFileSet0.030.020.06
mapToMammal406.080.567.27
matchDesign19.27 0.7720.11
meanIntensity2.760.253.22
medianTotalIntensity0.690.040.78
noMasked4.890.355.33
noob3.810.224.03
openSesame4.940.516.72
openSesameToFile4.280.164.44
pOOBAH1.890.122.02
palgen0.050.000.13
parseGEOsignalMU0.530.030.56
predictAgeHorvath3535.050.475.73
predictAgeSkinBlood4.060.254.38
predictMouseAgeInMonth3.520.283.94
prefixMask1.640.111.79
prefixMaskButC0.230.000.24
prefixMaskButCG0.090.000.09
prepSesame 9.58 0.6110.33
prepSesameList000
print.DMLSummary4.550.244.84
print.fileSet1.020.251.32
probeID_designType000
probeSuccessRate10.18 0.6111.01
qualityMask2.630.082.75
reIdentify4.420.094.56
readFileSet0.060.000.07
readIDATpair0.170.000.17
resetMask0.390.060.51
scrub5.070.245.30
scrubSoft5.860.396.25
sdfPlatform0.620.030.70
sdf_read_table11.61 0.4012.07
sdf_write_table8.140.208.39
searchIDATprefixes0.020.000.02
sesame-package2.590.072.70
sesameAnno_download000
sesameAnno_get000
sesameAnno_getManifestDF000
sesameData_getAnno000
sesameQC_calcStats29.49 1.0030.52
sesameQC_getStats2.340.062.40
sesameQC_plotBar13.25 0.6427.18
sesameQC_plotBetaByDesign14.84 0.8115.65
sesameQC_plotHeatSNPs24.61 0.9525.61
sesameQC_plotIntensVsBetas1.860.192.09
sesameQC_plotRedGrnQQ1.200.191.47
sesameQC_rankStats2.990.313.41
setMask0.220.000.22
signalMU0.690.100.83
sliceFileSet0.030.000.05
summaryExtractTest3.970.214.26
testEnrichment7.830.638.63
testEnrichmentGSEA 9.40 0.6110.96
totalIntensities2.420.152.77
updateSigDF2.650.275.08
visualizeGene8.750.409.27
visualizeProbes4.600.104.73
visualizeRegion0.640.000.64
visualizeSegments1.590.091.82