R Under development (unstable) (2026-02-03 r89375 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(metadeconfoundR)
Loading required package: detectseparation
> 
> test_check("metadeconfoundR")
Loading required package: ggplot2
starting worker pid=57284 on localhost:11861 at 15:29:36.995
starting worker pid=11488 on localhost:11861 at 15:29:37.541
WARN [2026-02-04 15:29:39] 
	Unallowed characters detected in rownames and/or colnames of featureMat and/or metaMat!
	metadeconfoundR will try to remove these characters using the make.names() function.
WARN [2026-02-04 15:29:39] adjustLevel not specified, setting to 3:
                                 multiple testing p-value correction over the number of
                                 features AND number of varables in mediationMat.
starting worker pid=60884 on localhost:11861 at 15:29:39.698
starting worker pid=103964 on localhost:11861 at 15:29:40.995
WARN [2026-02-04 15:29:41] lrt:  MS0038 Status Metformin -- forward linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0.
WARN [2026-02-04 15:29:41] lrt:  MS0038 Metformin Status -- reverse linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0.
ERROR [2026-02-04 15:29:42] adjustLevel == 3 not possible without supplying mediationMat.
ERROR [2026-02-04 15:29:42] mediationMat and metaMat don't have same number of rows.
ERROR [2026-02-04 15:29:42] rownames of mediationMat and metaMat don't have same order.
INFO [2026-02-04 15:29:42] 
	###
	###
	Deconfounding run started
WARN [2026-02-04 15:29:42] 
	Unallowed characters detected in rownames and/or colnames of featureMat and/or metaMat!
	metadeconfoundR will try to remove these characters using the make.names() function.
INFO [2026-02-04 15:29:42] Computing in serial mode. Set nnodes > 1 do to switch to faster parallel processing.
INFO [2026-02-04 15:29:42] Checking robustness of data for covariates
INFO [2026-02-04 15:29:42] Computation of naive associations started.
starting worker pid=62816 on localhost:11861 at 15:29:42.697
INFO [2026-02-04 15:29:42] NaiveAssociation -- processed 2% of features.
INFO [2026-02-04 15:29:42] NaiveAssociation -- processed 4% of features.
INFO [2026-02-04 15:29:42] NaiveAssociation -- processed 6% of features.
INFO [2026-02-04 15:29:42] NaiveAssociation -- processed 8% of features.
INFO [2026-02-04 15:29:42] NaiveAssociation -- processed 10% of features.
INFO [2026-02-04 15:29:42] NaiveAssociation -- processed 12% of features.
INFO [2026-02-04 15:29:42] NaiveAssociation -- processed 14% of features.
INFO [2026-02-04 15:29:42] NaiveAssociation -- processed 16% of features.
INFO [2026-02-04 15:29:42] NaiveAssociation -- processed 18% of features.
INFO [2026-02-04 15:29:42] NaiveAssociation -- processed 20% of features.
INFO [2026-02-04 15:29:42] NaiveAssociation -- processed 22% of features.
INFO [2026-02-04 15:29:42] NaiveAssociation -- processed 24% of features.
INFO [2026-02-04 15:29:42] NaiveAssociation -- processed 26% of features.
INFO [2026-02-04 15:29:42] NaiveAssociation -- processed 28% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 30% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 32% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 34% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 36% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 38% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 40% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 42% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 44% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 46% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 48% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 50% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 52% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 54% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 56% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 58% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 60% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 62% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 64% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 66% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 68% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 70% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 72% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 74% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 76% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 78% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 80% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 82% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 84% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 86% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 88% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 90% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 92% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 94% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 96% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 98% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 100% of features.
INFO [2026-02-04 15:29:43] NaiveAssociation -- processed 100% of features.
starting worker pid=23708 on localhost:11861 at 15:29:43.752
INFO [2026-02-04 15:29:43] Deconfounding -- processed 2% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 4% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 6% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 8% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 10% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 12% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 14% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 16% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 18% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 20% of features.
WARN [2026-02-04 15:29:44] lrt:  MS0038 Status Metformin -- forward linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0.
WARN [2026-02-04 15:29:44] lrt:  MS0038 Metformin Status -- reverse linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 22% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 24% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 26% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 28% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 30% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 32% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 34% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 36% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 38% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 40% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 42% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 44% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 46% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 48% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 50% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 52% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 54% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 56% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 58% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 60% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 62% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 64% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 66% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 68% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 70% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 72% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 74% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 76% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 78% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 80% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 82% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 84% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 86% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 88% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 90% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 92% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 94% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 96% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 98% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 100% of features.
INFO [2026-02-04 15:29:44] Deconfounding -- processed 100% of features.
INFO [2026-02-04 15:29:44] Removing 'confounded confounders' from status labels. Set noConfConfs = FALSE to keep them.
INFO [2026-02-04 15:29:44] MetadecondoundR run completed successfully!
INFO [2026-02-04 15:29:44] 
	###
	###
	Deconfounding run started
WARN [2026-02-04 15:29:44] 
	Unallowed characters detected in rownames and/or colnames of featureMat and/or metaMat!
	metadeconfoundR will try to remove these characters using the make.names() function.
INFO [2026-02-04 15:29:44] Computing in serial mode. Set nnodes > 1 do to switch to faster parallel processing.
INFO [2026-02-04 15:29:44] Checking robustness of data for covariates
INFO [2026-02-04 15:29:44] Computation of naive associations started.
starting worker pid=75900 on localhost:11861 at 15:29:45.127
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 2% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 4% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 6% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 8% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 10% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 12% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 14% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 16% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 18% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 20% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 22% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 24% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 26% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 28% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 30% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 32% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 34% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 36% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 38% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 40% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 42% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 44% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 46% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 48% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 50% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 52% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 54% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 56% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 58% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 60% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 62% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 64% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 66% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 68% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 70% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 72% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 74% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 76% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 78% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 80% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 82% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 84% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 86% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 88% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 90% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 92% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 94% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 96% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 98% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 100% of features.
INFO [2026-02-04 15:29:45] NaiveAssociation -- processed 100% of features.
starting worker pid=108320 on localhost:11861 at 15:29:45.668
INFO [2026-02-04 15:29:45] Deconfounding -- processed 2% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 4% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 6% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 8% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 10% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 12% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 14% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 16% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 18% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 20% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 22% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 24% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 26% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 28% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 30% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 32% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 34% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 36% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 38% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 40% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 42% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 44% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 46% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 48% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 50% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 52% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 54% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 56% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 58% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 60% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 62% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 64% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 66% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 68% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 70% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 72% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 74% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 76% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 78% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 80% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 82% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 84% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 86% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 88% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 90% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 92% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 94% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 96% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 98% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 100% of features.
INFO [2026-02-04 15:29:45] Deconfounding -- processed 100% of features.
INFO [2026-02-04 15:29:45] Removing 'confounded confounders' from status labels. Set noConfConfs = FALSE to keep them.
INFO [2026-02-04 15:29:45] MetadecondoundR run completed successfully!
starting worker pid=37696 on localhost:11861 at 15:29:46.164
starting worker pid=31644 on localhost:11861 at 15:29:47.212
starting worker pid=32156 on localhost:11861 at 15:29:48.532
starting worker pid=72504 on localhost:11861 at 15:29:49.849
INFO [2026-02-04 15:29:50] 
	###
	###
	Deconfounding run started
WARN [2026-02-04 15:29:50] 
	Unallowed characters detected in rownames and/or colnames of featureMat and/or metaMat!
	metadeconfoundR will try to remove these characters using the make.names() function.
INFO [2026-02-04 15:29:50] Computing in serial mode. Set nnodes > 1 do to switch to faster parallel processing.
INFO [2026-02-04 15:29:50] Checking robustness of data for covariates
WARN [2026-02-04 15:29:50] Naive p-values are NOT computed, but simply are a copy of the supplied adjusted p-values (QValues).
WARN [2026-02-04 15:29:50] Confonding status is computed based on Q-values and effect sizes supplied via "QValue" and "DValue" parameters. 
starting worker pid=99872 on localhost:11861 at 15:29:50.939
INFO [2026-02-04 15:29:51] Deconfounding -- processed 2% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 4% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 6% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 8% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 10% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 12% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 14% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 16% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 18% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 20% of features.
WARN [2026-02-04 15:29:51] lrt:  MS0038 Status Metformin -- forward linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0.
WARN [2026-02-04 15:29:51] lrt:  MS0038 Metformin Status -- reverse linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 22% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 24% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 26% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 28% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 30% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 32% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 34% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 36% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 38% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 40% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 42% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 44% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 46% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 48% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 50% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 52% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 54% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 56% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 58% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 60% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 62% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 64% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 66% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 68% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 70% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 72% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 74% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 76% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 78% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 80% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 82% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 84% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 86% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 88% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 90% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 92% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 94% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 96% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 98% of features.
INFO [2026-02-04 15:29:51] Deconfounding -- processed 100% of features.
INFO [2026-02-04 15:29:52] Deconfounding -- processed 100% of features.
INFO [2026-02-04 15:29:52] Removing 'confounded confounders' from status labels. Set noConfConfs = FALSE to keep them.
INFO [2026-02-04 15:29:52] MetadecondoundR run completed successfully!
starting worker pid=73936 on localhost:11861 at 15:29:52.211
starting worker pid=64152 on localhost:11861 at 15:29:52.213
Loading required package: metadeconfoundR
Loading required package: detectseparation
Loading required package: metadeconfoundR
Loading required package: detectseparation
loaded metadeconfoundR and set parent environment
loaded metadeconfoundR and set parent environment
INFO [2026-02-04 15:29:54] NaiveAssociation -- processed 2% of features.
INFO [2026-02-04 15:29:54] NaiveAssociation -- processed 4% of features.
INFO [2026-02-04 15:29:54] NaiveAssociation -- processed 6% of features.
INFO [2026-02-04 15:29:54] NaiveAssociation -- processed 8% of features.
INFO [2026-02-04 15:29:54] NaiveAssociation -- processed 10% of features.
INFO [2026-02-04 15:29:54] NaiveAssociation -- processed 12% of features.
INFO [2026-02-04 15:29:54] NaiveAssociation -- processed 14% of features.
INFO [2026-02-04 15:29:54] NaiveAssociation -- processed 16% of features.
INFO [2026-02-04 15:29:54] NaiveAssociation -- processed 18% of features.
INFO [2026-02-04 15:29:54] NaiveAssociation -- processed 20% of features.
INFO [2026-02-04 15:29:54] NaiveAssociation -- processed 22% of features.
INFO [2026-02-04 15:29:54] NaiveAssociation -- processed 24% of features.
INFO [2026-02-04 15:29:54] NaiveAssociation -- processed 26% of features.
INFO [2026-02-04 15:29:54] NaiveAssociation -- processed 28% of features.
INFO [2026-02-04 15:29:54] NaiveAssociation -- processed 30% of features.
INFO [2026-02-04 15:29:54] NaiveAssociation -- processed 32% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 34% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 36% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 38% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 40% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 42% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 44% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 46% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 48% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 50% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 52% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 54% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 56% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 58% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 60% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 62% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 64% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 66% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 68% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 70% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 72% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 74% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 76% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 78% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 82% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 80% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 86% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 84% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 90% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 88% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 92% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 94% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 96% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 100% of features.
INFO [2026-02-04 15:29:55] NaiveAssociation -- processed 98% of features.
starting worker pid=58052 on localhost:11861 at 15:29:55.452
starting worker pid=48768 on localhost:11861 at 15:29:55.458
Loading required package: metadeconfoundR
Loading required package: detectseparation
Loading required package: metadeconfoundR
Loading required package: detectseparation
loaded metadeconfoundR and set parent environment
loaded metadeconfoundR and set parent environment
INFO [2026-02-04 15:29:58] Deconfounding -- processed 4% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 2% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 8% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 6% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 10% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 12% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 14% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 16% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 18% of features.
WARN [2026-02-04 15:29:58] lrt:  MS0038 Status Metformin -- forward linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 20% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 24% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 26% of features.
WARN [2026-02-04 15:29:58] lrt:  MS0038 Metformin Status -- reverse linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 22% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 30% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 28% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 34% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 32% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 38% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 40% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 36% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 42% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 46% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 48% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 50% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 44% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 52% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 56% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 58% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 54% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 62% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 64% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 66% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 68% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 60% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 72% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 74% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 76% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 78% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 80% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 82% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 70% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 86% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 88% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 84% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 90% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 94% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 92% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 98% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 100% of features.
INFO [2026-02-04 15:29:58] Deconfounding -- processed 96% of features.
starting worker pid=4692 on localhost:11861 at 15:29:59.041
starting worker pid=102340 on localhost:11861 at 15:29:59.071
Loading required package: metadeconfoundR
Loading required package: detectseparation
Loading required package: metadeconfoundR
Loading required package: detectseparation
loaded metadeconfoundR and set parent environment
loaded metadeconfoundR and set parent environment
INFO [2026-02-04 15:30:01] NaiveAssociation -- processed 2% of features.
INFO [2026-02-04 15:30:01] NaiveAssociation -- processed 4% of features.
INFO [2026-02-04 15:30:01] NaiveAssociation -- processed 6% of features.
INFO [2026-02-04 15:30:01] NaiveAssociation -- processed 8% of features.
INFO [2026-02-04 15:30:01] NaiveAssociation -- processed 10% of features.
INFO [2026-02-04 15:30:01] NaiveAssociation -- processed 12% of features.
INFO [2026-02-04 15:30:01] NaiveAssociation -- processed 14% of features.
INFO [2026-02-04 15:30:01] NaiveAssociation -- processed 16% of features.
INFO [2026-02-04 15:30:01] NaiveAssociation -- processed 18% of features.
INFO [2026-02-04 15:30:01] NaiveAssociation -- processed 20% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 22% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 24% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 26% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 28% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 30% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 32% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 34% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 36% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 38% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 40% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 42% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 44% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 46% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 48% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 50% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 52% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 54% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 56% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 58% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 60% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 62% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 64% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 66% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 68% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 70% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 72% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 74% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 76% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 78% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 80% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 82% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 84% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 86% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 88% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 90% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 92% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 94% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 96% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 98% of features.
INFO [2026-02-04 15:30:02] NaiveAssociation -- processed 100% of features.
starting worker pid=107644 on localhost:11861 at 15:30:02.514
starting worker pid=14056 on localhost:11861 at 15:30:02.514
Loading required package: metadeconfoundR
Loading required package: detectseparation
Loading required package: metadeconfoundR
Loading required package: detectseparation
loaded metadeconfoundR and set parent environment
loaded metadeconfoundR and set parent environment
INFO [2026-02-04 15:30:05] Deconfounding -- processed 4% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 6% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 2% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 8% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 10% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 12% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 16% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 14% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 18% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 20% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 24% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 26% of features.
WARN [2026-02-04 15:30:05] lrt:  MS0038 Status Metformin -- forward linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0.
WARN [2026-02-04 15:30:05] lrt:  MS0038 Metformin Status -- reverse linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 22% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 30% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 28% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 34% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 32% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 36% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 40% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 38% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 44% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 42% of features.
INFO [2026-02-04 15:30:05] Deconfounding -- processed 48% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 50% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 52% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 46% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 56% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 58% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 54% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 62% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 64% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 66% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 68% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 60% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 72% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 74% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 76% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 78% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 70% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 80% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 82% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 86% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 88% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 84% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 90% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 94% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 92% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 98% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 100% of features.
INFO [2026-02-04 15:30:06] Deconfounding -- processed 96% of features.
starting worker pid=43160 on localhost:11861 at 15:30:06.661
starting worker pid=86908 on localhost:11861 at 15:30:07.655
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
WARN [2026-02-04 15:30:19] 
	Unallowed characters detected in rownames and/or colnames of featureMat and/or metaMat!
	metadeconfoundR will try to remove these characters using the make.names() function.
WARN [2026-02-04 15:30:19] collectMods was set to TRUE, model building step is run with nnodes = 1.
WARN [2026-02-04 15:30:19] the following random effect covariates will be excluded as potential donfounders: Dataset
WARN [2026-02-04 15:30:19] naive associations reducible to these efects will get the status label 'NS', while output elements Ps, Qs, and Ds will be unchanged.
starting worker pid=38108 on localhost:11861 at 15:30:19.349
WARN [2026-02-04 15:30:19] collectMods == TRUE --> setting nnodes = 1 for model building phase.
starting worker pid=20676 on localhost:11861 at 15:30:19.640
WARN [2026-02-04 15:30:21] Collected models are part ouf output. Only use output[["stdOutput"]] as BuildHeatmap input!
WARN [2026-02-04 15:30:21] 
	Unallowed characters detected in rownames and/or colnames of featureMat and/or metaMat!
	metadeconfoundR will try to remove these characters using the make.names() function.
WARN [2026-02-04 15:30:21] collectMods was set to TRUE, model building step is run with nnodes = 1.
WARN [2026-02-04 15:30:21] the following random effect covariates will be excluded as potential donfounders: Dataset
WARN [2026-02-04 15:30:21] naive associations reducible to these efects will get the status label 'NS', while output elements Ps, Qs, and Ds will be unchanged.
starting worker pid=29776 on localhost:11861 at 15:30:22.132
WARN [2026-02-04 15:30:22] collectMods == TRUE --> setting nnodes = 1 for model building phase.
starting worker pid=35480 on localhost:11861 at 15:30:22.428
INFO [2026-02-04 15:30:24] 
	###
	###
	Deconfounding run started
WARN [2026-02-04 15:30:24] 
	Unallowed characters detected in rownames and/or colnames of featureMat and/or metaMat!
	metadeconfoundR will try to remove these characters using the make.names() function.
INFO [2026-02-04 15:30:24] Computing in serial mode. Set nnodes > 1 do to switch to faster parallel processing.
INFO [2026-02-04 15:30:24] The following parameters will be added to all linear models as fixed effects: 'continuous_dummy'
INFO [2026-02-04 15:30:24] continuous_dummy
WARN [2026-02-04 15:30:24] the following fixed effect covariates will be excluded as potential donfounders: continuous_dummy
WARN [2026-02-04 15:30:24] naive associations reducible to these efects will get the status label 'NS', while output elements Ps, Qs, and Ds will be unchanged.
INFO [2026-02-04 15:30:24] Checking robustness of data for covariates
INFO [2026-02-04 15:30:24] 1 covariates where marked as too sparse and won't be considered in further analysis due to lack of sufficient data: continuous_dummy
INFO [2026-02-04 15:30:24] Computation of naive associations started.
starting worker pid=49080 on localhost:11861 at 15:30:24.928
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 2% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 4% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 6% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 8% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 10% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 12% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 14% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 16% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 18% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 20% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 22% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 24% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 26% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 28% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 30% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 32% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 34% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 36% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 38% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 40% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 42% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 44% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 46% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 48% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 50% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 52% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 54% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 56% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 58% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 60% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 62% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 64% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 66% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 68% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 70% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 72% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 74% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 76% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 78% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 80% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 82% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 84% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 86% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 88% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 90% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 92% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 94% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 96% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 98% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 100% of features.
INFO [2026-02-04 15:30:25] NaiveAssociation -- processed 100% of features.
starting worker pid=32796 on localhost:11861 at 15:30:25.936
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 2% of features.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 4% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 6% of features.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 8% of features.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 10% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 12% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 14% of features.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 16% of features.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 18% of features.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 20% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 22% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 24% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 26% of features.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 28% of features.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 30% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 32% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 34% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 36% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 38% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 40% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 42% of features.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 44% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 46% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 48% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 50% of features.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 52% of features.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 54% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 56% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 58% of features.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 60% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 62% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 64% of features.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:26] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 66% of features.
INFO [2026-02-04 15:30:26] Deconfounding -- processed 68% of features.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 70% of features.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 72% of features.
WARN [2026-02-04 15:30:27] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:27] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 74% of features.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 76% of features.
WARN [2026-02-04 15:30:27] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:27] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 78% of features.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 80% of features.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 82% of features.
WARN [2026-02-04 15:30:27] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:27] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 84% of features.
WARN [2026-02-04 15:30:27] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:27] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 86% of features.
WARN [2026-02-04 15:30:27] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:27] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 88% of features.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 90% of features.
WARN [2026-02-04 15:30:27] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:27] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 92% of features.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 94% of features.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 96% of features.
WARN [2026-02-04 15:30:27] In full model containing: (Intercept), DatasetMHD, DatasetSWE, altered_dummy, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
WARN [2026-02-04 15:30:27] In full model containing: (Intercept), altered_dummy, DatasetMHD, DatasetSWE, continuous_dummy, NA coefficient(s) are present: continuous_dummy. Setting forward and reverse LRTs to non-significant.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 98% of features.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 100% of features.
INFO [2026-02-04 15:30:27] Deconfounding -- processed 100% of features.
INFO [2026-02-04 15:30:27] Removing 'confounded confounders' from status labels. Set noConfConfs = FALSE to keep them.
INFO [2026-02-04 15:30:27] MetadecondoundR run completed successfully!
INFO [2026-02-04 15:30:27] 
	###
	###
	Deconfounding run started
WARN [2026-02-04 15:30:27] 
	Unallowed characters detected in rownames and/or colnames of featureMat and/or metaMat!
	metadeconfoundR will try to remove these characters using the make.names() function.
INFO [2026-02-04 15:30:27] Computing in serial mode. Set nnodes > 1 do to switch to faster parallel processing.
INFO [2026-02-04 15:30:27] The following parameters will be added to all linear models as random effects: 'Dataset'
INFO [2026-02-04 15:30:27] Dataset
WARN [2026-02-04 15:30:27] the following random effect covariates will be excluded as potential donfounders: Dataset
WARN [2026-02-04 15:30:27] naive associations reducible to these efects will get the status label 'NS', while output elements Ps, Qs, and Ds will be unchanged.
INFO [2026-02-04 15:30:27] The following parameters will be added to all linear models as fixed effects: 'continuous_dummy'
INFO [2026-02-04 15:30:27] continuous_dummy
WARN [2026-02-04 15:30:27] the following fixed effect covariates will be excluded as potential donfounders: Dataset, continuous_dummy
WARN [2026-02-04 15:30:27] naive associations reducible to these efects will get the status label 'NS', while output elements Ps, Qs, and Ds will be unchanged.
INFO [2026-02-04 15:30:27] Checking robustness of data for covariates
INFO [2026-02-04 15:30:27] 2 covariates where marked as too sparse and won't be considered in further analysis due to lack of sufficient data: Dataset, continuous_dummy
INFO [2026-02-04 15:30:27] Computation of naive associations started.
starting worker pid=15220 on localhost:11861 at 15:30:27.607
INFO [2026-02-04 15:30:27] NaiveAssociation -- processed 6.67% of features.
INFO [2026-02-04 15:30:27] NaiveAssociation -- processed 13.33% of features.
INFO [2026-02-04 15:30:27] NaiveAssociation -- processed 20% of features.
INFO [2026-02-04 15:30:27] NaiveAssociation -- processed 26.67% of features.
INFO [2026-02-04 15:30:27] NaiveAssociation -- processed 33.33% of features.
INFO [2026-02-04 15:30:27] NaiveAssociation -- processed 40% of features.
INFO [2026-02-04 15:30:27] NaiveAssociation -- processed 46.67% of features.
INFO [2026-02-04 15:30:27] NaiveAssociation -- processed 53.33% of features.
INFO [2026-02-04 15:30:27] NaiveAssociation -- processed 60% of features.
INFO [2026-02-04 15:30:27] NaiveAssociation -- processed 66.67% of features.
INFO [2026-02-04 15:30:27] NaiveAssociation -- processed 73.33% of features.
INFO [2026-02-04 15:30:27] NaiveAssociation -- processed 80% of features.
INFO [2026-02-04 15:30:27] NaiveAssociation -- processed 86.67% of features.
INFO [2026-02-04 15:30:27] NaiveAssociation -- processed 93.33% of features.
INFO [2026-02-04 15:30:27] NaiveAssociation -- processed 100% of features.
INFO [2026-02-04 15:30:27] NaiveAssociation -- processed 100% of features.
starting worker pid=21328 on localhost:11861 at 15:30:28.033
INFO [2026-02-04 15:30:29] Deconfounding -- processed 6.67% of features.
INFO [2026-02-04 15:30:29] Deconfounding -- processed 13.33% of features.
INFO [2026-02-04 15:30:30] Deconfounding -- processed 20% of features.
INFO [2026-02-04 15:30:30] Deconfounding -- processed 26.67% of features.
INFO [2026-02-04 15:30:30] Deconfounding -- processed 33.33% of features.
INFO [2026-02-04 15:30:31] Deconfounding -- processed 40% of features.
INFO [2026-02-04 15:30:31] Deconfounding -- processed 46.67% of features.
INFO [2026-02-04 15:30:31] Deconfounding -- processed 53.33% of features.
INFO [2026-02-04 15:30:31] Deconfounding -- processed 60% of features.
INFO [2026-02-04 15:30:31] Deconfounding -- processed 66.67% of features.
INFO [2026-02-04 15:30:32] Deconfounding -- processed 73.33% of features.
INFO [2026-02-04 15:30:32] Deconfounding -- processed 80% of features.
INFO [2026-02-04 15:30:32] Deconfounding -- processed 86.67% of features.
INFO [2026-02-04 15:30:32] Deconfounding -- processed 93.33% of features.
INFO [2026-02-04 15:30:32] Deconfounding -- processed 100% of features.
INFO [2026-02-04 15:30:32] Deconfounding -- processed 100% of features.
INFO [2026-02-04 15:30:32] Removing 'confounded confounders' from status labels. Set noConfConfs = FALSE to keep them.
INFO [2026-02-04 15:30:32] MetadecondoundR run completed successfully!
WARN [2026-02-04 15:30:32] 
	Unallowed characters detected in rownames and/or colnames of featureMat and/or metaMat!
	metadeconfoundR will try to remove these characters using the make.names() function.
WARN [2026-02-04 15:30:32] collectMods was set to TRUE, model building step is run with nnodes = 1.
starting worker pid=3484 on localhost:11861 at 15:30:32.664
WARN [2026-02-04 15:30:32] Separation for: MS0035 and Status
WARN [2026-02-04 15:30:32] Separation for: MS0035 and Dataset
WARN [2026-02-04 15:30:32] Separation for: MS0035 and Metformin
WARN [2026-02-04 15:30:33] collectMods == TRUE --> setting nnodes = 1 for model building phase.
starting worker pid=3448 on localhost:11861 at 15:30:33.198
WARN [2026-02-04 15:30:33] Collected models are part ouf output. Only use output[["stdOutput"]] as BuildHeatmap input!
starting worker pid=91588 on localhost:11861 at 15:30:33.539
starting worker pid=83892 on localhost:11861 at 15:30:34.654
INFO [2026-02-04 15:31:08] 
	###
	###
	Deconfounding run started
WARN [2026-02-04 15:31:08] 
	Unallowed characters detected in rownames and/or colnames of featureMat and/or metaMat!
	metadeconfoundR will try to remove these characters using the make.names() function.
WARN [2026-02-04 15:31:08] Raw count mode is enabled!For computation of naive associations only, raw counts are being normalized by dividing each sample by its total count! 
INFO [2026-02-04 15:31:08] Computing in serial mode. Set nnodes > 1 do to switch to faster parallel processing.
INFO [2026-02-04 15:31:08] The following parameters will be added to all linear models as random effects: 'Dataset'
INFO [2026-02-04 15:31:08] Dataset
WARN [2026-02-04 15:31:08] the following random effect covariates will be excluded as potential donfounders: Dataset
WARN [2026-02-04 15:31:08] naive associations reducible to these efects will get the status label 'NS', while output elements Ps, Qs, and Ds will be unchanged.
INFO [2026-02-04 15:31:08] Checking robustness of data for covariates
INFO [2026-02-04 15:31:08] 1 covariates where marked as too sparse and won't be considered in further analysis due to lack of sufficient data: Dataset
INFO [2026-02-04 15:31:08] Computation of naive associations started.
starting worker pid=93536 on localhost:11861 at 15:31:08.438
INFO [2026-02-04 15:31:08] NaiveAssociation -- processed 20% of features.
INFO [2026-02-04 15:31:08] NaiveAssociation -- processed 40% of features.
INFO [2026-02-04 15:31:08] NaiveAssociation -- processed 60% of features.
INFO [2026-02-04 15:31:08] NaiveAssociation -- processed 80% of features.
INFO [2026-02-04 15:31:08] NaiveAssociation -- processed 100% of features.
INFO [2026-02-04 15:31:08] NaiveAssociation -- processed 100% of features.
starting worker pid=63836 on localhost:11861 at 15:31:08.759
INFO [2026-02-04 15:31:52] Deconfounding -- processed 20% of features.
INFO [2026-02-04 15:32:00] Deconfounding -- processed 40% of features.
INFO [2026-02-04 15:32:16] Deconfounding -- processed 60% of features.
INFO [2026-02-04 15:32:16] Deconfounding -- processed 80% of features.
INFO [2026-02-04 15:32:17] Deconfounding -- processed 100% of features.
INFO [2026-02-04 15:32:17] Deconfounding -- processed 100% of features.
INFO [2026-02-04 15:32:17] Removing 'confounded confounders' from status labels. Set noConfConfs = FALSE to keep them.
INFO [2026-02-04 15:32:17] MetadecondoundR run completed successfully!
ERROR [2026-02-04 15:32:17] Necessary argument "metaMat" missing.
ERROR [2026-02-04 15:32:17] Necessary argument "featureMat" missing.
ERROR [2026-02-04 15:32:17] featureMat and metaMat don't have same number of rows.
ERROR [2026-02-04 15:32:17] rownames of featureMat and metaMat don't have same order.
INFO [2026-02-04 15:32:17] 
	###
	###
	Deconfounding run started
WARN [2026-02-04 15:32:17] 
	Unallowed characters detected in rownames and/or colnames of featureMat and/or metaMat!
	metadeconfoundR will try to remove these characters using the make.names() function.
ERROR [2026-02-04 15:32:17] Elements of deconfT/deconfF are not present in colnames of metaMat.
INFO [2026-02-04 15:32:17] Check identical spelling of variable
                      names in deconfT/deconfF and metaMat
ERROR [2026-02-04 15:32:17] Some elements of deconfT and deconfF seem to be identical.
ERROR [2026-02-04 15:32:17] rawCounts and logistic can not be both set to TRUE!
ERROR [2026-02-04 15:32:17] QValues and/or DValues argument is supplied but seems to be empty (NULL).
ERROR [2026-02-04 15:32:17] randomVar does not need to be supplied as list anymore, please change to new syntax.
ERROR [2026-02-04 15:32:17] Not enough (robustCutoff = 5 ) samples for either case (== 1) or control (== 0) group in metaMat column one ( Status ). Make sure column one of metaMat is a binary (0/1) variable.
ERROR [2026-02-04 15:32:17] Non-numeric columns detected in featureMat.
INFO [2026-02-04 15:32:17] 
	###
	###
	Deconfounding run started
WARN [2026-02-04 15:32:17] 
	Unallowed characters detected in rownames and/or colnames of featureMat and/or metaMat!
	metadeconfoundR will try to remove these characters using the make.names() function.
INFO [2026-02-04 15:32:17] Computing in serial mode. Set nnodes > 1 do to switch to faster parallel processing.
INFO [2026-02-04 15:32:17] Checking robustness of data for covariates
INFO [2026-02-04 15:32:17] Computation of naive associations started.
starting worker pid=38812 on localhost:11861 at 15:32:17.447
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 2% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 4% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 6% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 8% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 10% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 12% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 14% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 16% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 18% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 20% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 22% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 24% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 26% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 28% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 30% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 32% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 34% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 36% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 38% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 40% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 42% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 44% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 46% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 48% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 50% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 52% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 54% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 56% of features.
INFO [2026-02-04 15:32:17] NaiveAssociation -- processed 58% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 60% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 62% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 64% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 66% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 68% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 70% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 72% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 74% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 76% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 78% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 80% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 82% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 84% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 86% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 88% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 90% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 92% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 94% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 96% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 98% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 100% of features.
INFO [2026-02-04 15:32:18] NaiveAssociation -- processed 100% of features.
starting worker pid=49276 on localhost:11861 at 15:32:18.508
INFO [2026-02-04 15:32:18] Deconfounding -- processed 2% of features.
INFO [2026-02-04 15:32:18] Deconfounding -- processed 4% of features.
INFO [2026-02-04 15:32:18] Deconfounding -- processed 6% of features.
INFO [2026-02-04 15:32:18] Deconfounding -- processed 8% of features.
INFO [2026-02-04 15:32:18] Deconfounding -- processed 10% of features.
INFO [2026-02-04 15:32:18] Deconfounding -- processed 12% of features.
INFO [2026-02-04 15:32:18] Deconfounding -- processed 14% of features.
INFO [2026-02-04 15:32:18] Deconfounding -- processed 16% of features.
INFO [2026-02-04 15:32:18] Deconfounding -- processed 18% of features.
INFO [2026-02-04 15:32:18] Deconfounding -- processed 20% of features.
WARN [2026-02-04 15:32:18] lrt:  MS0038 Status Metformin -- forward linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0.
WARN [2026-02-04 15:32:18] lrt:  MS0038 Metformin Status -- reverse linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0.
INFO [2026-02-04 15:32:18] Deconfounding -- processed 22% of features.
INFO [2026-02-04 15:32:18] Deconfounding -- processed 24% of features.
INFO [2026-02-04 15:32:18] Deconfounding -- processed 26% of features.
INFO [2026-02-04 15:32:18] Deconfounding -- processed 28% of features.
INFO [2026-02-04 15:32:18] Deconfounding -- processed 30% of features.
INFO [2026-02-04 15:32:18] Deconfounding -- processed 32% of features.
INFO [2026-02-04 15:32:18] Deconfounding -- processed 34% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 36% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 38% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 40% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 42% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 44% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 46% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 48% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 50% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 52% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 54% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 56% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 58% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 60% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 62% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 64% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 66% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 68% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 70% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 72% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 74% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 76% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 78% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 80% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 82% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 84% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 86% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 88% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 90% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 92% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 94% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 96% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 98% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 100% of features.
INFO [2026-02-04 15:32:19] Deconfounding -- processed 100% of features.
INFO [2026-02-04 15:32:19] Removing 'confounded confounders' from status labels. Set noConfConfs = FALSE to keep them.
INFO [2026-02-04 15:32:19] MetadecondoundR run completed successfully!
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 66 ]
> 
> proc.time()
   user  system elapsed 
 154.92    1.89  175.81