##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:dnaEPICO.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings dnaEPICO_0.99.17.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/dnaEPICO.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-15 03:20:17 UTC
* checking for file ‘dnaEPICO/DESCRIPTION’ ... OK
* this is package ‘dnaEPICO’ version ‘0.99.17’
* 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 ‘dnaEPICO’ 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 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
filterProbesMinfiEwasWater  41.491  3.032  44.525
preprocessingMinfiEwasWater 34.380  1.361  35.760
assessSamplesMinfiEwasWater 24.244  0.850  25.120
dnamReport                  14.522  1.735  13.036
svaEnmix                     7.369  0.112   7.482
normalizeMinfiEwasWater      7.179  0.180   7.359
readRGSetMinfiEwasWater      6.814  0.359   7.173
analyzeSvaEnmix              5.639  0.228   5.867
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL dnaEPICO
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘dnaEPICO’ ...
** this is package ‘dnaEPICO’ version ‘0.99.17’
** 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 (dnaEPICO)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(dnaEPICO)
> 
> test_check("dnaEPICO")
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

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

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: 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: 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

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: locfit
locfit 1.5-9.12 	 2025-03-05
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Plotting  STAINING .jpg 
Plotting  EXTENSION .jpg 
Plotting  HYBRIDIZATION .jpg 
Plotting  TARGET_REMOVAL .jpg 
Plotting  BISULFITE_CONVERSION_I .jpg 
Plotting  BISULFITE_CONVERSION_II .jpg 
Plotting  SPECIFICITY_I .jpg 
Plotting  SPECIFICITY_II .jpg 
Plotting  NON-POLYMORPHIC .jpg 
Plotting  NEGATIVE .jpg 
Plotting  NORM_A .jpg 
Plotting  NORM_C .jpg 
Plotting  NORM_G .jpg 
Plotting  NORM_T .jpg 
Plotting  NORM_ACGT .jpg 
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
[adjustedFunnorm] Background and dye bias correction with noob
[adjustedFunnorm] Mapping to genome
[adjustedFunnorm] Quantile extraction
[adjustedFunnorm] Normalization
3  surrogate variables explain  91.17398 % of 
    data variation
  adding: beta.csv (deflated 55%)
fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
Start time:                      2026-05-14 23:27:32
Input phenotype + beta:          /tmp/Rtmpnjev5N/filed58d935ee665c/phenoBetaT1T2.RData
Output RData folder:             /tmp/Rtmpnjev5N/filed58d935ee665c/rData/methylationGLMM_T1T2/models
Output logs folder:              /tmp/Rtmpnjev5N/filed58d935ee665c/logs
Output plots folder:             /tmp/Rtmpnjev5N/filed58d935ee665c/figures/methylationGLMM_T1T2
Person ID variable:              person
Time variable:                   Timepoint
Phenotypes:                      score
Covariates:                      sex
Factor variables:                sex,Timepoint
LME libraries:                   lme4,lmerTest
PRS mapping:                     None
CpG column prefix:               cg
CpG limit:                       2
Number of cores:                 1
Summary p-value filter:          1
Interaction term:                None
Save significant interactions:   TRUE
Significant interaction p-value: 1
Save text summaries:             TRUE
Chunk size:                      Auto
FDR threshold:                   0.05
P-value adjustment method:       fdr
Display plots:                   FALSE
Verbose messages:                TRUE
Write logs:                      TRUE
Save outputs:                    TRUE
=======================================================================
=======================================================================
Loaded longitudinal phenotype + beta data from: /tmp/Rtmpnjev5N/filed58d935ee665c/phenoBetaT1T2.RData
Data dimensions:                   8 x 7
Person variable:                   person
Time variable:                     Timepoint
Phenotypes:                        score
Covariates:                        sex
Factor variables:                  sex, Timepoint
CpG columns retained:              2
Created person variable from SID:  person
Count of records per person ID:

1 2 3 4 
2 2 2 2 
Values observed in Timepoint :

1 2 
4 4 
Example mapping of SID to person ID:
  SID person
1 P1A      1
2 P1B      1
3 P2A      2
4 P2B      2
5 P3A      3
6 P3B      3
Summary statistics for phenotype scores by timepoint:
  Timepoint score_mean score_sd score_n
1         1       10.0 2.160247       4
2         2       11.5 2.081666       4
=======================================================================
=======================================================================
Fitted phenotype:             score
Formula:                      beta ~ `score` + `Timepoint` + `sex` + (1 | `person` )
CpGs attempted:               2
Failed CpG fits:              0
=======================================================================
=======================================================================
Summarized phenotype:         score
LME summary rows returned:    2
Summary chunk size:           10
P-value filter:               1
=======================================================================
=======================================================================
Significant longitudinal terms retained at p < 1 :
score: 2
=======================================================================
=======================================================================
Diagnostic plots generated for phenotypes: 1
Diagnostic plots saved to:     /tmp/Rtmpnjev5N/filed58d935ee665c/figures/methylationGLMM_T1T2
=======================================================================
=======================================================================
Annotated CpG rows:           2
Annotation columns used:       Name, chr, pos
Missing annotation columns:   none
=======================================================================
=======================================================================
Serialized model outputs:     1
Serialized summary outputs:   1
Annotated results file:       /tmp/Rtmpnjev5N/filed58d935ee665c/data/methylationGLMM_T1T2/annotatedLME.csv
Summary text files written:    1
Significant interaction files: 2
=======================================================================
=======================================================================
Finished DNAm LME Analysis (Timepoint 1 vs 2): 2026-05-14 23:27:33
Annotated LME output:           /tmp/Rtmpnjev5N/filed58d935ee665c/data/methylationGLMM_T1T2/annotatedLME.csv
=======================================================================
Start time:                 2026-05-14 23:27:34
Input phenotype + beta:     /tmp/Rtmpnjev5N/filed58d962a2ae87/phenoBetaT1.RData
Output RData folder:        /tmp/Rtmpnjev5N/filed58d962a2ae87/rData/methylationGLM_T1/models
Output logs folder:         /tmp/Rtmpnjev5N/filed58d962a2ae87/logs
Output plots folder:        /tmp/Rtmpnjev5N/filed58d962a2ae87/figures/methylationGLM_T1
Phenotypes:                 status
Covariates:                 sex
Factor variables:           status,sex
CpG column prefix:          cg
CpG limit:                  2
Number of cores:            1
Interaction term:           None
GLM libraries:              glm2
PRS mapping:                None
Summary p-value filter:     1
Include Residual SD:        TRUE
Chunk size:                 Auto
FDR threshold:              0.05
P-value adjustment method:  fdr
Display plots:              FALSE
Verbose messages:           TRUE
Write logs:                 TRUE
Save outputs:               TRUE
=======================================================================
=======================================================================
Loaded phenotype + beta data from: /tmp/Rtmpnjev5N/filed58d962a2ae87/phenoBetaT1.RData
Data dimensions:              4 x 5
Phenotypes:                   status
Covariates:                   sex
Factor variables:             status, sex
CpG columns retained:         2
Missing summary:
status: 0; sex: 0
Summary statistics:
     status  sex  
 Case   :2   F:2  
 Control:2   M:2  
=======================================================================
=======================================================================
Phenotype distribution plots:  1
Factor distribution plots:     2
Numeric covariate plots:       0
Distribution plots saved to:   /tmp/Rtmpnjev5N/filed58d962a2ae87/figures/methylationGLM_T1
=======================================================================
=======================================================================
Fitted phenotype:             status
Formula:                      beta ~ `status` + `sex`
CpGs attempted:               2
Failed CpG fits:              0
=======================================================================
=======================================================================
Summarized phenotype:         status
CpG summary rows returned:    2
Summary chunk size:           10
P-value filter:               1
=======================================================================
=======================================================================
Significant CpGs retained at p < 1 :
status: 2
=======================================================================
=======================================================================
Diagnostic plots generated for phenotypes: 1
Diagnostic plots saved to:     /tmp/Rtmpnjev5N/filed58d962a2ae87/figures/methylationGLM_T1
=======================================================================
=======================================================================
Annotated CpG rows:           2
Annotation columns used:       Name, chr, pos
Missing annotation columns:   none
=======================================================================
=======================================================================
Serialized model outputs:     1
Serialized summary outputs:   1
Annotated results file:       /tmp/Rtmpnjev5N/filed58d962a2ae87/data/methylationGLM_T1/annotatedGLM.csv
Summary text files written:    1
Significant CpG text files:   2
=======================================================================
=======================================================================
Finished DNAm GLM Analysis (Timepoint 1): 2026-05-14 23:27:36
Annotated GLM output:          /tmp/Rtmpnjev5N/filed58d962a2ae87/data/methylationGLM_T1/annotatedGLM.csv
=======================================================================
Start Time:                2026-05-14 23:27:37
Log file path:             /tmp/Rtmpnjev5N/filed58d93e38f52f/logs/log_preprocessingPheno.txt
Phenotype file:            /tmp/Rtmpnjev5N/filed58d93e38f52f/pheno.csv
Separator type:            default (',')
Beta path:                 /tmp/Rtmpnjev5N/filed58d93e38f52f/beta.RData
M-values path:             /tmp/Rtmpnjev5N/filed58d93e38f52f/m.RData
CN path:                   /tmp/Rtmpnjev5N/filed58d93e38f52f/cn.RData
Identifier column:         Sample_Name
Timepoint column:          Timepoint
Timepoints:                1,2
Combine timepoints:        1,2
Sex column:                Sex
Output phenotype dir:      /tmp/Rtmpnjev5N/filed58d93e38f52f/data/preprocessingPheno
RData metrics dir:         /tmp/Rtmpnjev5N/filed58d93e38f52f/rData/preprocessingPheno/metrics
RData merge dir:           /tmp/Rtmpnjev5N/filed58d93e38f52f/rData/preprocessingPheno/mergeData
Clock Foundation dir:      /tmp/Rtmpnjev5N/filed58d93e38f52f/clockFoundation
Verbose messages:          TRUE
Write logs:                TRUE
Save outputs:              TRUE
=======================================================================
=======================================================================
Phenotype file:            /tmp/Rtmpnjev5N/filed58d93e38f52f/pheno.csv
Separator type:            default (',')
SampleID column:           Sample_Name
nSamples limit:            all
Using all 3 samples.
Phenotype file loaded with 3 samples and 3 columns.
Preview of targets:
  Sample_Name Timepoint Sex
1          S1         1   0
2          S2         1   1
3          S3         2   0
=======================================================================
=======================================================================
Beta path:                 /tmp/Rtmpnjev5N/filed58d93e38f52f/beta.RData
M-values path:             /tmp/Rtmpnjev5N/filed58d93e38f52f/m.RData
CN path:                   /tmp/Rtmpnjev5N/filed58d93e38f52f/cn.RData
Beta dimensions:           2 x 3
M dimensions:              2 x 3
CN dimensions:             2 x 3
Preview of beta values:
     S1  S2  S3
cg1 0.1 0.3 0.5
cg2 0.2 0.4 0.6
=======================================================================
Requested timepoints:       1, 2
Available values in Timepoint column:

1 2 
2 1 
Timepoint 1 rows:          2
Timepoint  1  matched samples: 2
Timepoint 2 rows:          1
Timepoint  2  matched samples: 1
=======================================================================
Combining timepoints:       1, 2
Combined phenotype rows:    3
Combined phenoBeta rows:    3
Combined suffix:            T1T2
=======================================================================
Clock Foundation beta rows: 2
Clock Foundation beta cols: 4
Clock Foundation pheno rows: 3
Re-encoding Sex: 0 = Female, 1 = Male
Preview of Clock Foundation beta table:
  ProbeID  S1  S2  S3
1     cg1 0.1 0.3 0.5
2     cg2 0.2 0.4 0.6
=======================================================================
  adding: beta.csv (deflated 25%)
Output phenotype dir:      /tmp/Rtmpnjev5N/filed58d93e38f52f/data/preprocessingPheno
RData metrics dir:         /tmp/Rtmpnjev5N/filed58d93e38f52f/rData/preprocessingPheno/metrics
RData merge dir:           /tmp/Rtmpnjev5N/filed58d93e38f52f/rData/preprocessingPheno/mergeData
Clock Foundation dir:      /tmp/Rtmpnjev5N/filed58d93e38f52f/clockFoundation
Saved combined phenotype:  /tmp/Rtmpnjev5N/filed58d93e38f52f/data/preprocessingPheno/phenoT1T2.csv
Saved combined phenoBeta:  /tmp/Rtmpnjev5N/filed58d93e38f52f/rData/preprocessingPheno/mergeData/phenoBetaT1T2.RData
Saved beta CSV:            /tmp/Rtmpnjev5N/filed58d93e38f52f/clockFoundation/beta.csv
Saved beta ZIP:            /tmp/Rtmpnjev5N/filed58d93e38f52f/clockFoundation/beta.zip
Saved phenoCF:             /tmp/Rtmpnjev5N/filed58d93e38f52f/clockFoundation/phenoCF.csv
ZIP status code:           0
=======================================================================
==== Finished preprocessingPheno ====
End Time:                  2026-05-14 23:27:37
=======================================================================
=======================================================================
Phenotype file:            /tmp/Rtmpnjev5N/filed58d94e0c6503.csv
Separator type:            default (',')
SampleID column:           Sample_Name
nSamples limit:            all
Using all 2 samples.
Preview of targets:
  Sample_Name Sex
1          S1   F
2          S2   M
=======================================================================
3  surrogate variables explain  100 % of 
    data variation
3  surrogate variables explain  100 % of 
    data variation
[ FAIL 0 | WARN 39 | SKIP 0 | PASS 169 ]

[ FAIL 0 | WARN 39 | SKIP 0 | PASS 169 ]
> 
> proc.time()
   user  system elapsed 
255.548  10.293 258.771