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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sesame_1.23.8.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    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 ‘1.23.8’
* 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            49.211  0.898  63.259
imputeBetasByGenomicNeighbors 45.143  0.655  49.168
inferSex                      31.353  0.219  33.786
imputeBetas                   30.330  0.574  34.289
sesameQC_calcStats            30.230  0.119  31.479
KYCG_plotMeta                 26.741  0.296  30.290
sesameQC_plotHeatSNPs         26.099  0.206  27.449
ELBAR                         23.438  0.323  24.896
KYCG_plotEnrichAll            22.665  0.518  30.740
sesameQC_plotBetaByDesign     18.927  0.124  19.092
matchDesign                   18.070  0.212  19.435
KYCG_annoProbes               16.436  0.431  20.365
inferSpecies                  16.360  0.427  20.047
compareMouseStrainReference   16.497  0.147  18.826
diffRefSet                    16.111  0.208  18.698
compareReference              15.320  0.176  17.677
testEnrichmentSEA             14.789  0.131  18.270
KYCG_plotMetaEnrichment       14.116  0.296  17.650
sesameQC_plotBar              12.894  0.193  15.288
getRefSet                     12.585  0.211  14.979
KYCG_buildGeneDBs             11.931  0.224  14.359
DMR                           11.021  0.307  13.499
inferStrain                   11.013  0.275  13.460
visualizeGene                 10.187  0.223  13.623
inferTissue                   10.043  0.331  12.780
DML                            9.184  0.380  11.754
estimateLeukocyte              9.045  0.193  11.441
sdf_read_table                 9.036  0.152  11.329
dyeBiasNL                      9.104  0.047  10.223
KYCG_plotSetEnrichment         8.262  0.175  10.598
dbStats                        8.075  0.132  10.474
getMask                        7.819  0.216  12.331
deidentify                     7.839  0.068  10.070
probeSuccessRate               6.772  0.131  10.119
scrubSoft                      6.840  0.020   6.875
openSesame                     6.737  0.116   9.038
testEnrichment                 6.483  0.160   9.865
createUCSCtrack                6.473  0.112   8.741
reIdentify                     6.364  0.048   7.513
dyeBiasCorrMostBalanced        6.242  0.128   8.532
prepSesame                     5.811  0.092   6.985
bisConversionControl           5.131  0.084   7.367
sesameQC_rankStats             5.070  0.080   7.298
updateSigDF                    4.497  0.107   6.749
noMasked                       4.245  0.128   6.522
mapToMammal40                  3.845  0.143   6.169
checkLevels                    3.855  0.100   5.048
parseGEOsignalMU               3.844  0.092   5.032
dyeBiasCorr                    3.752  0.064   5.970
summaryExtractTest             3.572  0.151   5.850
totalIntensities               3.530  0.096   5.896
print.DMLSummary               3.483  0.116   5.768
meanIntensity                  3.443  0.072   5.648
KYCG_getDBs                    3.235  0.092   5.470
qualityMask                    3.014  0.091   5.237
* 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

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL sesame
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/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)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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 
 23.401   0.989  26.565