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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dnaEPICO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dnaEPICO_0.99.17.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/dnaEPICO.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-19 01:18:39 UTC
* using option ‘--no-vignettes’
* 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 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  16.387  0.144  16.611
preprocessingMinfiEwasWater 12.149  0.187  12.407
assessSamplesMinfiEwasWater  9.576  0.207   9.815
dnamReport                   7.365  1.313   7.623
* 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/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 Patched (2026-05-01 r89994) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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:                      2026-05-18 21:21:45
Input phenotype + beta:          /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf73a0af359/phenoBetaT1T2.RData
Output RData folder:             /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf73a0af359/rData/methylationGLMM_T1T2/models
Output logs folder:              /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf73a0af359/logs
Output plots folder:             /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf73a0af359/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: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf73a0af359/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:     /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf73a0af359/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:       /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf73a0af359/data/methylationGLMM_T1T2/annotatedLME.csv
Summary text files written:    1
Significant interaction files: 2
=======================================================================
=======================================================================
Finished DNAm LME Analysis (Timepoint 1 vs 2): 2026-05-18 21:21:45
Annotated LME output:           /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf73a0af359/data/methylationGLMM_T1T2/annotatedLME.csv
=======================================================================
Start time:                 2026-05-18 21:21:45
Input phenotype + beta:     /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf76679fe02/phenoBetaT1.RData
Output RData folder:        /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf76679fe02/rData/methylationGLM_T1/models
Output logs folder:         /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf76679fe02/logs
Output plots folder:        /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf76679fe02/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: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf76679fe02/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:   /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf76679fe02/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:     /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf76679fe02/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:       /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf76679fe02/data/methylationGLM_T1/annotatedGLM.csv
Summary text files written:    1
Significant CpG text files:   2
=======================================================================
=======================================================================
Finished DNAm GLM Analysis (Timepoint 1): 2026-05-18 21:21:46
Annotated GLM output:          /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf76679fe02/data/methylationGLM_T1/annotatedGLM.csv
=======================================================================
Start Time:                2026-05-18 21:21:46
Log file path:             /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpQinbGO/file14bf72aeec643/logs/log_preprocessingPheno.txt
Phenotype file:            /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/pheno.csv
Separator type:            default (',')
Beta path:                 /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/beta.RData
M-values path:             /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/m.RData
CN path:                   /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/cn.RData
Identifier column:         Sample_Name
Timepoint column:          Timepoint
Timepoints:                1,2
Combine timepoints:        1,2
Sex column:                Sex
Output phenotype dir:      /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/data/preprocessingPheno
RData metrics dir:         /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/rData/preprocessingPheno/metrics
RData merge dir:           /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/rData/preprocessingPheno/mergeData
Clock Foundation dir:      /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/clockFoundation
Verbose messages:          TRUE
Write logs:                TRUE
Save outputs:              TRUE
=======================================================================
=======================================================================
Phenotype file:            /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/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:                 /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/beta.RData
M-values path:             /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/m.RData
CN path:                   /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/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:      /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/data/preprocessingPheno
RData metrics dir:         /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/rData/preprocessingPheno/metrics
RData merge dir:           /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/rData/preprocessingPheno/mergeData
Clock Foundation dir:      /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/clockFoundation
Saved combined phenotype:  /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/data/preprocessingPheno/phenoT1T2.csv
Saved combined phenoBeta:  /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/rData/preprocessingPheno/mergeData/phenoBetaT1T2.RData
Saved beta CSV:            /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/clockFoundation/beta.csv
Saved beta ZIP:            /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/clockFoundation/beta.zip
Saved phenoCF:             /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf72aeec643/clockFoundation/phenoCF.csv
ZIP status code:           0
=======================================================================
==== Finished preprocessingPheno ====
End Time:                  2026-05-18 21:21:46
=======================================================================
=======================================================================
Phenotype file:            /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQinbGO/file14bf785ba04d.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 
109.791   4.131 112.411