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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MEAT.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MEAT_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MEAT.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MEAT/DESCRIPTION’ ... OK
* this is package ‘MEAT’ version ‘1.11.0’
* 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 ‘MEAT’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
* 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 ... NOTE
Killed
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Killed
Killed
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... WARNING
  LazyData DB of 5.7 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MEAT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BMIQcalibration
> ### Title: Calibrate methylation data to a gold standard.
> ### Aliases: BMIQcalibration
> 
> ### ** Examples
> 
> # Load matrix of beta-values of two individuals from dataset GSE121961
> data("GSE121961", envir = environment())
> # Load phenotypes of the two individuals from dataset GSE121961
> data("GSE121961_pheno", envir = environment())
> 
> # Create a SummarizedExperiment object to coordinate phenotypes and
> # methylation into one object.
> library(SummarizedExperiment)
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
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: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

> GSE121961_SE <- SummarizedExperiment(assays=list(beta=GSE121961),
+ colData=GSE121961_pheno)
> 
> # Run clean_beta() to clean the beta-matrix
> GSE121961_SE_clean <- clean_beta(SE = GSE121961_SE, version = "MEAT2.0")
-------------------Step 1-------------------------------
Reducing your beta-matrix to the 18747 CpGs used to calibrate methylation profiles in MEAT2.0
Your beta-matrix contains 18747 of the 18747 CpGs needed to calibrate methylation profiles.
-------------------Step 2-------------------------------
Checking for missing values in the beta-matrix.
Your beta-matrix contains 70 missing values.
Warning in knnimp(x, k, maxmiss = rowmax, maxp = maxp) :
  35 rows with more than 50 % entries missing;
 mean imputation used for these rows
Cluster size 18712 broken into 13355 5357 
Cluster size 13355 broken into 1809 11546 
Cluster size 1809 broken into 872 937 
Done cluster 872 
Done cluster 937 
Done cluster 1809 
Cluster size 11546 broken into 4355 7191 
Cluster size 4355 broken into 3154 1201 
Cluster size 3154 broken into 1997 1157 
Cluster size 1997 broken into 1497 500 
Done cluster 1497 
Done cluster 500 
Done cluster 1997 
Done cluster 1157 
Done cluster 3154 
Done cluster 1201 
Done cluster 4355 
Cluster size 7191 broken into 2960 4231 
Cluster size 2960 broken into 1555 1405 
Cluster size 1555 broken into 546 1009 
Done cluster 546 
Done cluster 1009 
Done cluster 1555 
Done cluster 1405 
Done cluster 2960 
Cluster size 4231 broken into 3042 1189 
Cluster size 3042 broken into 2094 948 
Cluster size 2094 broken into 1061 1033 
Done cluster 1061 
Done cluster 1033 
Done cluster 2094 
Done cluster 948 
Done cluster 3042 
Done cluster 1189 
Done cluster 4231 
Done cluster 7191 
Done cluster 11546 
Done cluster 13355 
Cluster size 5357 broken into 3289 2068 
Cluster size 3289 broken into 1295 1994 
Done cluster 1295 
Cluster size 1994 broken into 988 1006 
Done cluster 988 
Done cluster 1006 
Done cluster 1994 
Done cluster 3289 
Cluster size 2068 broken into 1043 1025 
Done cluster 1043 
Done cluster 1025 
Done cluster 2068 
Done cluster 5357 
-------------------Step 3-------------------------------
Checking for the presence of 0 and 1.
Your beta-matrix contains 0 0 values and 0 1 values.
> 
> # Run BMIQcalibration() to calibrate the clean beta-matrix
> GSE121961_SE_calibrated <- BMIQcalibration(SE = GSE121961_SE_clean, version = "MEAT2.0")
Fitting EM beta mixture to goldstandard probes.
[1] Inf
[1] 0.001738881
[1] 0.00248846
[1] 0.002669617
[1] 0.002586372
Done
ii= 1
Fitting EM beta mixture to input probes
Killed
* 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 ...
  ‘MEAT.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘MEAT.Rmd’ using knitr
Killed

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/MEAT.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MEAT
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘MEAT’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package can be loaded from final location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package keeps a record of temporary installation path
* DONE (MEAT)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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(MEAT)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
> 
> test_check("MEAT")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 21.017   0.849  22.884