R Under development (unstable) (2026-01-10 r89298 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=40180 on localhost:11997 at 10:26:41.673 starting worker pid=30796 on localhost:11997 at 10:26:42.517 boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') WARN [2026-01-12 10:26:47] 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 [2026-01-12 10:26:47] 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=103140 on localhost:11997 at 10:26:47.957 starting worker pid=18748 on localhost:11997 at 10:26:49.859 WARN [2026-01-12 10:26:50] lrt: MS0038 Status Metformin -- forward linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0. WARN [2026-01-12 10:26:50] lrt: MS0038 Metformin Status -- reverse linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0. ERROR [2026-01-12 10:26:51] adjustLevel == 3 not possible without supplying mediationMat. ERROR [2026-01-12 10:26:51] mediationMat and metaMat don't have same number of rows. ERROR [2026-01-12 10:26:51] rownames of mediationMat and metaMat don't have same order. INFO [2026-01-12 10:26:51] ### ### Deconfounding run started WARN [2026-01-12 10:26:51] 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 [2026-01-12 10:26:51] Computing in serial mode. Set nnodes > 1 do to switch to faster parallel processing. INFO [2026-01-12 10:26:51] Checking robustness of data for covariates INFO [2026-01-12 10:26:51] Computation of naive associations started. starting worker pid=40892 on localhost:11997 at 10:26:52.163 INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 2% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 4% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 6% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 8% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 10% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 12% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 14% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 16% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 18% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 20% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 22% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 24% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 26% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 28% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 30% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 32% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 34% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 36% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 38% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 40% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 42% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 44% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 46% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 48% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 50% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 52% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 54% of features. INFO [2026-01-12 10:26:52] NaiveAssociation -- processed 56% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 58% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 60% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 62% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 64% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 66% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 68% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 70% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 72% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 74% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 76% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 78% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 80% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 82% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 84% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 86% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 88% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 90% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 92% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 94% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 96% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 98% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 100% of features. INFO [2026-01-12 10:26:53] NaiveAssociation -- processed 100% of features. starting worker pid=59372 on localhost:11997 at 10:26:53.811 INFO [2026-01-12 10:26:54] Deconfounding -- processed 2% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 4% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 6% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 8% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 10% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 12% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 14% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 16% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 18% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 20% of features. WARN [2026-01-12 10:26:54] lrt: MS0038 Status Metformin -- forward linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0. WARN [2026-01-12 10:26:54] lrt: MS0038 Metformin Status -- reverse linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0. INFO [2026-01-12 10:26:54] Deconfounding -- processed 22% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 24% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 26% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 28% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 30% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 32% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 34% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 36% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 38% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 40% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 42% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 44% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 46% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 48% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 50% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 52% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 54% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 56% of features. INFO [2026-01-12 10:26:54] Deconfounding -- processed 58% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 60% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 62% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 64% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 66% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 68% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 70% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 72% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 74% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 76% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 78% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 80% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 82% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 84% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 86% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 88% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 90% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 92% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 94% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 96% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 98% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:26:55] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:26:55] Removing 'confounded confounders' from status labels. Set noConfConfs = FALSE to keep them. INFO [2026-01-12 10:26:55] MetadecondoundR run completed successfully! INFO [2026-01-12 10:26:55] ### ### Deconfounding run started WARN [2026-01-12 10:26:55] 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 [2026-01-12 10:26:55] Computing in serial mode. Set nnodes > 1 do to switch to faster parallel processing. INFO [2026-01-12 10:26:55] Checking robustness of data for covariates INFO [2026-01-12 10:26:55] Computation of naive associations started. starting worker pid=72136 on localhost:11997 at 10:26:56.036 INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 2% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 4% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 6% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 8% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 10% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 12% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 14% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 16% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 18% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 20% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 22% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 24% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 26% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 28% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 30% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 32% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 34% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 36% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 38% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 40% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 42% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 44% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 46% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 48% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 50% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 52% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 54% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 56% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 58% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 60% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 62% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 64% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 66% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 68% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 70% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 72% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 74% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 76% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 78% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 80% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 82% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 84% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 86% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 88% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 90% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 92% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 94% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 96% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 98% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 100% of features. INFO [2026-01-12 10:26:56] NaiveAssociation -- processed 100% of features. starting worker pid=26020 on localhost:11997 at 10:26:56.862 INFO [2026-01-12 10:26:57] Deconfounding -- processed 2% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 4% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 6% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 8% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 10% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 12% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 14% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 16% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 18% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 20% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 22% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 24% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 26% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 28% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 30% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 32% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 34% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 36% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 38% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 40% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 42% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 44% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 46% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 48% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 50% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 52% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 54% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 56% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 58% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 60% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 62% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 64% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 66% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 68% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 70% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 72% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 74% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 76% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 78% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 80% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 82% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 84% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 86% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 88% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 90% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 92% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 94% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 96% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 98% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:26:57] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:26:57] Removing 'confounded confounders' from status labels. Set noConfConfs = FALSE to keep them. INFO [2026-01-12 10:26:57] MetadecondoundR run completed successfully! starting worker pid=46224 on localhost:11997 at 10:26:57.615 starting worker pid=47924 on localhost:11997 at 10:26:59.262 starting worker pid=51784 on localhost:11997 at 10:27:01.476 starting worker pid=88528 on localhost:11997 at 10:27:03.203 INFO [2026-01-12 10:27:04] ### ### Deconfounding run started WARN [2026-01-12 10:27:04] 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 [2026-01-12 10:27:04] Computing in serial mode. Set nnodes > 1 do to switch to faster parallel processing. INFO [2026-01-12 10:27:04] Checking robustness of data for covariates WARN [2026-01-12 10:27:04] Naive p-values are NOT computed, but simply are a copy of the supplied adjusted p-values (QValues). WARN [2026-01-12 10:27:04] Confonding status is computed based on Q-values and effect sizes supplied via "QValue" and "DValue" parameters. starting worker pid=40892 on localhost:11997 at 10:27:04.908 INFO [2026-01-12 10:27:05] Deconfounding -- processed 2% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 4% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 6% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 8% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 10% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 12% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 14% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 16% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 18% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 20% of features. WARN [2026-01-12 10:27:05] lrt: MS0038 Status Metformin -- forward linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0. WARN [2026-01-12 10:27:05] lrt: MS0038 Metformin Status -- reverse linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0. INFO [2026-01-12 10:27:05] Deconfounding -- processed 22% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 24% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 26% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 28% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 30% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 32% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 34% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 36% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 38% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 40% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 42% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 44% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 46% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 48% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 50% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 52% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 54% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 56% of features. INFO [2026-01-12 10:27:05] Deconfounding -- processed 58% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 60% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 62% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 64% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 66% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 68% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 70% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 72% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 74% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 76% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 78% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 80% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 82% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 84% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 86% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 88% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 90% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 92% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 94% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 96% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 98% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:27:06] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:27:06] Removing 'confounded confounders' from status labels. Set noConfConfs = FALSE to keep them. INFO [2026-01-12 10:27:06] MetadecondoundR run completed successfully! starting worker pid=38424 on localhost:11997 at 10:27:06.853 starting worker pid=45824 on localhost:11997 at 10:27:06.867 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 [2026-01-12 10:27:11] NaiveAssociation -- processed 4% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 2% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 6% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 8% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 12% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 10% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 14% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 16% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 18% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 22% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 20% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 26% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 24% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 30% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 28% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 32% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 36% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 34% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 38% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 40% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 42% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 44% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 46% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 48% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 52% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 50% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 54% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 56% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 58% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 60% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 62% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 64% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 66% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 70% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 68% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 72% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 74% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 76% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 80% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 78% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 82% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 84% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 86% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 88% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 90% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 94% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 92% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 96% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 98% of features. INFO [2026-01-12 10:27:11] NaiveAssociation -- processed 100% of features. starting worker pid=9564 on localhost:11997 at 10:27:11.964 starting worker pid=101304 on localhost:11997 at 10:27:11.981 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 [2026-01-12 10:27:16] Deconfounding -- processed 4% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 2% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 6% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 8% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 10% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 12% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 16% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 14% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 18% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 20% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 24% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 26% of features. WARN [2026-01-12 10:27:16] lrt: MS0038 Status Metformin -- forward linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0. WARN [2026-01-12 10:27:16] lrt: MS0038 Metformin Status -- reverse linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0. INFO [2026-01-12 10:27:16] Deconfounding -- processed 22% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 30% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 28% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 34% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 32% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 38% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 40% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 36% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 44% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 42% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 48% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 50% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 52% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 46% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 56% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 58% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 54% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 62% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 64% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 60% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 68% of features. INFO [2026-01-12 10:27:16] Deconfounding -- processed 70% of features. INFO [2026-01-12 10:27:17] Deconfounding -- processed 66% of features. INFO [2026-01-12 10:27:17] Deconfounding -- processed 72% of features. INFO [2026-01-12 10:27:17] Deconfounding -- processed 76% of features. INFO [2026-01-12 10:27:17] Deconfounding -- processed 74% of features. INFO [2026-01-12 10:27:17] Deconfounding -- processed 78% of features. INFO [2026-01-12 10:27:17] Deconfounding -- processed 82% of features. INFO [2026-01-12 10:27:17] Deconfounding -- processed 80% of features. INFO [2026-01-12 10:27:17] Deconfounding -- processed 84% of features. INFO [2026-01-12 10:27:17] Deconfounding -- processed 86% of features. INFO [2026-01-12 10:27:17] Deconfounding -- processed 88% of features. INFO [2026-01-12 10:27:17] Deconfounding -- processed 90% of features. INFO [2026-01-12 10:27:17] Deconfounding -- processed 94% of features. INFO [2026-01-12 10:27:17] Deconfounding -- processed 92% of features. INFO [2026-01-12 10:27:17] Deconfounding -- processed 98% of features. INFO [2026-01-12 10:27:17] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:27:17] Deconfounding -- processed 96% of features. starting worker pid=18436 on localhost:11997 at 10:27:17.477 starting worker pid=96616 on localhost:11997 at 10:27:17.500 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 [2026-01-12 10:27:21] NaiveAssociation -- processed 2% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 4% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 6% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 8% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 10% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 12% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 14% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 16% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 18% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 20% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 22% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 24% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 26% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 28% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 30% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 32% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 34% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 36% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 38% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 40% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 42% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 44% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 46% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 48% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 50% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 52% of features. INFO [2026-01-12 10:27:21] NaiveAssociation -- processed 54% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 56% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 58% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 60% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 62% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 64% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 66% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 70% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 68% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 72% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 74% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 76% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 78% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 80% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 82% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 84% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 88% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 86% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 92% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 90% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 94% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 96% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 98% of features. INFO [2026-01-12 10:27:22] NaiveAssociation -- processed 100% of features. starting worker pid=27568 on localhost:11997 at 10:27:22.579 starting worker pid=24428 on localhost:11997 at 10:27:22.594 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 [2026-01-12 10:27:26] Deconfounding -- processed 4% of features. INFO [2026-01-12 10:27:26] Deconfounding -- processed 2% of features. INFO [2026-01-12 10:27:26] Deconfounding -- processed 8% of features. INFO [2026-01-12 10:27:26] Deconfounding -- processed 6% of features. INFO [2026-01-12 10:27:26] Deconfounding -- processed 10% of features. INFO [2026-01-12 10:27:26] Deconfounding -- processed 12% of features. INFO [2026-01-12 10:27:26] Deconfounding -- processed 14% of features. INFO [2026-01-12 10:27:26] Deconfounding -- processed 16% of features. INFO [2026-01-12 10:27:26] Deconfounding -- processed 18% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 20% of features. WARN [2026-01-12 10:27:27] lrt: MS0038 Status Metformin -- forward linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0. INFO [2026-01-12 10:27:27] Deconfounding -- processed 24% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 26% of features. WARN [2026-01-12 10:27:27] lrt: MS0038 Metformin Status -- reverse linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0. INFO [2026-01-12 10:27:27] Deconfounding -- processed 22% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 30% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 28% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 34% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 32% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 36% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 40% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 38% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 42% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 44% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 48% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 50% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 52% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 46% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 56% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 58% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 54% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 62% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 60% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 64% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 68% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 70% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 66% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 74% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 76% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 78% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 72% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 82% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 80% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 86% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 84% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 88% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 90% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 92% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 94% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 98% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:27:27] Deconfounding -- processed 96% of features. starting worker pid=28992 on localhost:11997 at 10:27:28.078 starting worker pid=79996 on localhost:11997 at 10:27:29.760 boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') WARN [2026-01-12 10:27:46] 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 [2026-01-12 10:27:46] collectMods was set to TRUE, model building step is run with nnodes = 1. WARN [2026-01-12 10:27:46] the following random effect covariates will be excluded as potential donfounders: Dataset WARN [2026-01-12 10:27:46] 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=18164 on localhost:11997 at 10:27:46.332 WARN [2026-01-12 10:27:46] collectMods == TRUE --> setting nnodes = 1 for model building phase. starting worker pid=110076 on localhost:11997 at 10:27:46.706 WARN [2026-01-12 10:27:50] Collected models are part ouf output. Only use output[["stdOutput"]] as BuildHeatmap input! WARN [2026-01-12 10:27:50] 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. WARN [2026-01-12 10:27:50] collectMods was set to TRUE, model building step is run with nnodes = 1. WARN [2026-01-12 10:27:50] the following random effect covariates will be excluded as potential donfounders: Dataset WARN [2026-01-12 10:27:50] 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=89636 on localhost:11997 at 10:27:50.411 WARN [2026-01-12 10:27:50] collectMods == TRUE --> setting nnodes = 1 for model building phase. starting worker pid=110644 on localhost:11997 at 10:27:50.866 INFO [2026-01-12 10:27:54] ### ### Deconfounding run started WARN [2026-01-12 10:27:54] 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 [2026-01-12 10:27:54] Computing in serial mode. Set nnodes > 1 do to switch to faster parallel processing. INFO [2026-01-12 10:27:54] The following parameters will be added to all linear models as fixed effects: 'continuous_dummy' INFO [2026-01-12 10:27:54] continuous_dummy WARN [2026-01-12 10:27:54] the following fixed effect covariates will be excluded as potential donfounders: continuous_dummy WARN [2026-01-12 10:27:54] naive associations reducible to these efects will get the status label 'NS', while output elements Ps, Qs, and Ds will be unchanged. INFO [2026-01-12 10:27:54] Checking robustness of data for covariates INFO [2026-01-12 10:27:54] 1 covariates where marked as too sparse and won't be considered in further analysis due to lack of sufficient data: continuous_dummy INFO [2026-01-12 10:27:54] Computation of naive associations started. starting worker pid=74912 on localhost:11997 at 10:27:54.683 INFO [2026-01-12 10:27:54] NaiveAssociation -- processed 2% of features. INFO [2026-01-12 10:27:54] NaiveAssociation -- processed 4% of features. INFO [2026-01-12 10:27:54] NaiveAssociation -- processed 6% of features. INFO [2026-01-12 10:27:54] NaiveAssociation -- processed 8% of features. INFO [2026-01-12 10:27:54] NaiveAssociation -- processed 10% of features. INFO [2026-01-12 10:27:54] NaiveAssociation -- processed 12% of features. INFO [2026-01-12 10:27:54] NaiveAssociation -- processed 14% of features. INFO [2026-01-12 10:27:54] NaiveAssociation -- processed 16% of features. INFO [2026-01-12 10:27:54] NaiveAssociation -- processed 18% of features. INFO [2026-01-12 10:27:54] NaiveAssociation -- processed 20% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 22% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 24% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 26% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 28% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 30% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 32% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 34% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 36% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 38% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 40% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 42% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 44% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 46% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 48% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 50% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 52% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 54% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 56% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 58% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 60% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 62% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 64% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 66% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 68% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 70% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 72% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 74% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 76% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 78% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 80% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 82% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 84% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 86% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 88% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 90% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 92% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 94% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 96% of features. INFO [2026-01-12 10:27:55] NaiveAssociation -- processed 98% of features. INFO [2026-01-12 10:27:56] NaiveAssociation -- processed 100% of features. INFO [2026-01-12 10:27:56] NaiveAssociation -- processed 100% of features. starting worker pid=58104 on localhost:11997 at 10:27:56.248 WARN [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] Deconfounding -- processed 2% of features. WARN [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] Deconfounding -- processed 4% of features. INFO [2026-01-12 10:27:56] Deconfounding -- processed 6% of features. WARN [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] Deconfounding -- processed 8% of features. WARN [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] Deconfounding -- processed 10% of features. INFO [2026-01-12 10:27:56] Deconfounding -- processed 12% of features. INFO [2026-01-12 10:27:56] Deconfounding -- processed 14% of features. WARN [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] Deconfounding -- processed 16% of features. WARN [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] Deconfounding -- processed 18% of features. WARN [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] Deconfounding -- processed 20% of features. INFO [2026-01-12 10:27:56] Deconfounding -- processed 22% of features. INFO [2026-01-12 10:27:56] Deconfounding -- processed 24% of features. INFO [2026-01-12 10:27:56] Deconfounding -- processed 26% of features. WARN [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] Deconfounding -- processed 28% of features. WARN [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] 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 [2026-01-12 10:27:56] Deconfounding -- processed 30% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 32% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 34% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 36% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 38% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 40% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 42% of features. WARN [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] Deconfounding -- processed 44% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 46% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 48% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 50% of features. WARN [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] Deconfounding -- processed 52% of features. WARN [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] Deconfounding -- processed 54% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 56% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 58% of features. WARN [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] Deconfounding -- processed 60% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 62% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 64% of features. WARN [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] Deconfounding -- processed 66% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 68% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 70% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 72% of features. WARN [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] Deconfounding -- processed 74% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 76% of features. WARN [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] Deconfounding -- processed 78% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 80% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 82% of features. WARN [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] Deconfounding -- processed 84% of features. WARN [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] Deconfounding -- processed 86% of features. WARN [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] Deconfounding -- processed 88% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 90% of features. WARN [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] 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 [2026-01-12 10:27:57] Deconfounding -- processed 92% of features. INFO [2026-01-12 10:27:57] Deconfounding -- processed 94% of features. INFO [2026-01-12 10:27:58] Deconfounding -- processed 96% of features. WARN [2026-01-12 10:27:58] 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 [2026-01-12 10:27:58] 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 [2026-01-12 10:27:58] Deconfounding -- processed 98% of features. INFO [2026-01-12 10:27:58] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:27:58] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:27:58] Removing 'confounded confounders' from status labels. Set noConfConfs = FALSE to keep them. INFO [2026-01-12 10:27:58] MetadecondoundR run completed successfully! INFO [2026-01-12 10:27:58] ### ### Deconfounding run started WARN [2026-01-12 10:27:58] 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 [2026-01-12 10:27:58] Computing in serial mode. Set nnodes > 1 do to switch to faster parallel processing. INFO [2026-01-12 10:27:58] The following parameters will be added to all linear models as random effects: 'Dataset' INFO [2026-01-12 10:27:58] Dataset WARN [2026-01-12 10:27:58] the following random effect covariates will be excluded as potential donfounders: Dataset WARN [2026-01-12 10:27:58] naive associations reducible to these efects will get the status label 'NS', while output elements Ps, Qs, and Ds will be unchanged. INFO [2026-01-12 10:27:58] The following parameters will be added to all linear models as fixed effects: 'continuous_dummy' INFO [2026-01-12 10:27:58] continuous_dummy WARN [2026-01-12 10:27:58] the following fixed effect covariates will be excluded as potential donfounders: Dataset, continuous_dummy WARN [2026-01-12 10:27:58] naive associations reducible to these efects will get the status label 'NS', while output elements Ps, Qs, and Ds will be unchanged. INFO [2026-01-12 10:27:58] Checking robustness of data for covariates INFO [2026-01-12 10:27:58] 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 [2026-01-12 10:27:58] Computation of naive associations started. starting worker pid=78860 on localhost:11997 at 10:27:58.347 INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 2% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 4% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 6% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 8% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 10% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 12% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 14% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 16% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 18% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 20% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 22% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 24% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 26% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 28% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 30% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 32% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 34% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 36% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 38% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 40% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 42% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 44% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 46% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 48% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 50% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 52% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 54% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 56% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 58% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 60% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 62% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 64% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 66% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 68% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 70% of features. INFO [2026-01-12 10:27:58] NaiveAssociation -- processed 72% of features. INFO [2026-01-12 10:27:59] NaiveAssociation -- processed 74% of features. INFO [2026-01-12 10:27:59] NaiveAssociation -- processed 76% of features. INFO [2026-01-12 10:27:59] NaiveAssociation -- processed 78% of features. INFO [2026-01-12 10:27:59] NaiveAssociation -- processed 80% of features. INFO [2026-01-12 10:27:59] NaiveAssociation -- processed 82% of features. INFO [2026-01-12 10:27:59] NaiveAssociation -- processed 84% of features. INFO [2026-01-12 10:27:59] NaiveAssociation -- processed 86% of features. INFO [2026-01-12 10:27:59] NaiveAssociation -- processed 88% of features. INFO [2026-01-12 10:27:59] NaiveAssociation -- processed 90% of features. INFO [2026-01-12 10:27:59] NaiveAssociation -- processed 92% of features. INFO [2026-01-12 10:27:59] NaiveAssociation -- processed 94% of features. INFO [2026-01-12 10:27:59] NaiveAssociation -- processed 96% of features. INFO [2026-01-12 10:27:59] NaiveAssociation -- processed 98% of features. INFO [2026-01-12 10:27:59] NaiveAssociation -- processed 100% of features. INFO [2026-01-12 10:27:59] NaiveAssociation -- processed 100% of features. starting worker pid=104800 on localhost:11997 at 10:27:59.554 INFO [2026-01-12 10:28:01] Deconfounding -- processed 2% of features. INFO [2026-01-12 10:28:02] Deconfounding -- processed 4% of features. INFO [2026-01-12 10:28:03] Deconfounding -- processed 6% of features. INFO [2026-01-12 10:28:03] Deconfounding -- processed 8% of features. INFO [2026-01-12 10:28:03] Deconfounding -- processed 10% of features. INFO [2026-01-12 10:28:04] Deconfounding -- processed 12% of features. INFO [2026-01-12 10:28:04] Deconfounding -- processed 14% of features. INFO [2026-01-12 10:28:05] Deconfounding -- processed 16% of features. INFO [2026-01-12 10:28:05] Deconfounding -- processed 18% of features. INFO [2026-01-12 10:28:05] Deconfounding -- processed 20% of features. INFO [2026-01-12 10:28:05] Deconfounding -- processed 22% of features. INFO [2026-01-12 10:28:05] Deconfounding -- processed 24% of features. INFO [2026-01-12 10:28:05] Deconfounding -- processed 26% of features. INFO [2026-01-12 10:28:06] Deconfounding -- processed 28% of features. INFO [2026-01-12 10:28:06] Deconfounding -- processed 30% of features. INFO [2026-01-12 10:28:07] Deconfounding -- processed 32% of features. INFO [2026-01-12 10:28:07] Deconfounding -- processed 34% of features. INFO [2026-01-12 10:28:08] Deconfounding -- processed 36% of features. INFO [2026-01-12 10:28:08] Deconfounding -- processed 38% of features. INFO [2026-01-12 10:28:08] Deconfounding -- processed 40% of features. INFO [2026-01-12 10:28:08] Deconfounding -- processed 42% of features. boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') INFO [2026-01-12 10:28:09] Deconfounding -- processed 44% of features. INFO [2026-01-12 10:28:10] Deconfounding -- processed 46% of features. INFO [2026-01-12 10:28:10] Deconfounding -- processed 48% of features. INFO [2026-01-12 10:28:10] Deconfounding -- processed 50% of features. INFO [2026-01-12 10:28:10] Deconfounding -- processed 52% of features. INFO [2026-01-12 10:28:11] Deconfounding -- processed 54% of features. INFO [2026-01-12 10:28:11] Deconfounding -- processed 56% of features. INFO [2026-01-12 10:28:11] Deconfounding -- processed 58% of features. boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') INFO [2026-01-12 10:28:13] Deconfounding -- processed 60% of features. INFO [2026-01-12 10:28:13] Deconfounding -- processed 62% of features. INFO [2026-01-12 10:28:13] Deconfounding -- processed 64% of features. boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') INFO [2026-01-12 10:28:14] Deconfounding -- processed 66% of features. INFO [2026-01-12 10:28:14] Deconfounding -- processed 68% of features. INFO [2026-01-12 10:28:15] Deconfounding -- processed 70% of features. INFO [2026-01-12 10:28:15] Deconfounding -- processed 72% of features. INFO [2026-01-12 10:28:15] Deconfounding -- processed 74% of features. INFO [2026-01-12 10:28:15] Deconfounding -- processed 76% of features. INFO [2026-01-12 10:28:15] Deconfounding -- processed 78% of features. INFO [2026-01-12 10:28:16] Deconfounding -- processed 80% of features. boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') INFO [2026-01-12 10:28:16] Deconfounding -- processed 82% of features. INFO [2026-01-12 10:28:17] Deconfounding -- processed 84% of features. INFO [2026-01-12 10:28:17] Deconfounding -- processed 86% of features. INFO [2026-01-12 10:28:17] Deconfounding -- processed 88% of features. INFO [2026-01-12 10:28:18] Deconfounding -- processed 90% of features. INFO [2026-01-12 10:28:19] Deconfounding -- processed 92% of features. INFO [2026-01-12 10:28:19] Deconfounding -- processed 94% of features. INFO [2026-01-12 10:28:20] Deconfounding -- processed 96% of features. boundary (singular) fit: see help('isSingular') INFO [2026-01-12 10:28:20] Deconfounding -- processed 98% of features. INFO [2026-01-12 10:28:20] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:28:20] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:28:20] Removing 'confounded confounders' from status labels. Set noConfConfs = FALSE to keep them. INFO [2026-01-12 10:28:20] MetadecondoundR run completed successfully! starting worker pid=53904 on localhost:11997 at 10:28:20.706 starting worker pid=79320 on localhost:11997 at 10:28:36.130 WARN [2026-01-12 10:28:47] 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 [2026-01-12 10:28:47] collectMods was set to TRUE, model building step is run with nnodes = 1. starting worker pid=88148 on localhost:11997 at 10:28:47.353 WARN [2026-01-12 10:28:47] Separation for: MS0035 and Status WARN [2026-01-12 10:28:47] Separation for: MS0035 and Dataset WARN [2026-01-12 10:28:47] Separation for: MS0035 and Metformin WARN [2026-01-12 10:28:47] collectMods == TRUE --> setting nnodes = 1 for model building phase. starting worker pid=105808 on localhost:11997 at 10:28:48.215 WARN [2026-01-12 10:28:48] Collected models are part ouf output. Only use output[["stdOutput"]] as BuildHeatmap input! starting worker pid=53356 on localhost:11997 at 10:28:48.740 starting worker pid=24628 on localhost:11997 at 10:29:03.761 INFO [2026-01-12 10:29:14] ### ### Deconfounding run started WARN [2026-01-12 10:29:14] 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 [2026-01-12 10:29:15] Computing in serial mode. Set nnodes > 1 do to switch to faster parallel processing. INFO [2026-01-12 10:29:15] The following parameters will be added to all linear models as random effects: 'Dataset' INFO [2026-01-12 10:29:15] Dataset WARN [2026-01-12 10:29:15] the following random effect covariates will be excluded as potential donfounders: Dataset WARN [2026-01-12 10:29:15] naive associations reducible to these efects will get the status label 'NS', while output elements Ps, Qs, and Ds will be unchanged. INFO [2026-01-12 10:29:15] Checking robustness of data for covariates INFO [2026-01-12 10:29:15] 1 covariates where marked as too sparse and won't be considered in further analysis due to lack of sufficient data: Dataset INFO [2026-01-12 10:29:15] Computation of naive associations started. starting worker pid=20852 on localhost:11997 at 10:29:15.245 INFO [2026-01-12 10:29:15] NaiveAssociation -- processed 6.67% of features. INFO [2026-01-12 10:29:15] NaiveAssociation -- processed 13.33% of features. INFO [2026-01-12 10:29:16] NaiveAssociation -- processed 20% of features. INFO [2026-01-12 10:29:16] NaiveAssociation -- processed 26.67% of features. INFO [2026-01-12 10:29:16] NaiveAssociation -- processed 33.33% of features. INFO [2026-01-12 10:29:16] NaiveAssociation -- processed 40% of features. INFO [2026-01-12 10:29:16] NaiveAssociation -- processed 46.67% of features. INFO [2026-01-12 10:29:16] NaiveAssociation -- processed 53.33% of features. WARN [2026-01-12 10:29:16] Separation for: MS0035 and Status WARN [2026-01-12 10:29:16] Separation for: MS0035 and Metformin INFO [2026-01-12 10:29:16] NaiveAssociation -- processed 60% of features. WARN [2026-01-12 10:29:17] Separation for: MS0037 and Status WARN [2026-01-12 10:29:17] Separation for: MS0037 and Metformin INFO [2026-01-12 10:29:17] NaiveAssociation -- processed 66.67% of features. INFO [2026-01-12 10:29:17] NaiveAssociation -- processed 73.33% of features. INFO [2026-01-12 10:29:17] NaiveAssociation -- processed 80% of features. INFO [2026-01-12 10:29:18] NaiveAssociation -- processed 86.67% of features. INFO [2026-01-12 10:29:18] NaiveAssociation -- processed 93.33% of features. INFO [2026-01-12 10:29:18] NaiveAssociation -- processed 100% of features. INFO [2026-01-12 10:29:18] NaiveAssociation -- processed 100% of features. starting worker pid=22340 on localhost:11997 at 10:29:19.069 INFO [2026-01-12 10:29:44] Deconfounding -- processed 6.67% of features. INFO [2026-01-12 10:29:44] Deconfounding -- processed 13.33% of features. INFO [2026-01-12 10:30:10] Deconfounding -- processed 20% of features. INFO [2026-01-12 10:30:10] Deconfounding -- processed 26.67% of features. INFO [2026-01-12 10:30:10] Deconfounding -- processed 33.33% of features. INFO [2026-01-12 10:30:34] Deconfounding -- processed 40% of features. INFO [2026-01-12 10:30:58] Deconfounding -- processed 46.67% of features. INFO [2026-01-12 10:30:58] Deconfounding -- processed 53.33% of features. INFO [2026-01-12 10:30:58] Deconfounding -- processed 60% of features. INFO [2026-01-12 10:30:58] Deconfounding -- processed 66.67% of features. INFO [2026-01-12 10:31:22] Deconfounding -- processed 73.33% of features. INFO [2026-01-12 10:31:22] Deconfounding -- processed 80% of features. INFO [2026-01-12 10:31:22] Deconfounding -- processed 86.67% of features. INFO [2026-01-12 10:31:22] Deconfounding -- processed 93.33% of features. INFO [2026-01-12 10:31:23] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:31:23] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:31:23] Removing 'confounded confounders' from status labels. Set noConfConfs = FALSE to keep them. INFO [2026-01-12 10:31:23] MetadecondoundR run completed successfully! INFO [2026-01-12 10:31:23] ### ### Deconfounding run started WARN [2026-01-12 10:31:23] 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 [2026-01-12 10:31:23] 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 [2026-01-12 10:31:23] Computing in serial mode. Set nnodes > 1 do to switch to faster parallel processing. INFO [2026-01-12 10:31:23] The following parameters will be added to all linear models as random effects: 'Dataset' INFO [2026-01-12 10:31:23] Dataset WARN [2026-01-12 10:31:23] the following random effect covariates will be excluded as potential donfounders: Dataset WARN [2026-01-12 10:31:23] naive associations reducible to these efects will get the status label 'NS', while output elements Ps, Qs, and Ds will be unchanged. INFO [2026-01-12 10:31:23] Checking robustness of data for covariates INFO [2026-01-12 10:31:23] 1 covariates where marked as too sparse and won't be considered in further analysis due to lack of sufficient data: Dataset INFO [2026-01-12 10:31:23] Computation of naive associations started. starting worker pid=3364 on localhost:11997 at 10:31:23.668 INFO [2026-01-12 10:31:23] NaiveAssociation -- processed 6.67% of features. INFO [2026-01-12 10:31:23] NaiveAssociation -- processed 13.33% of features. INFO [2026-01-12 10:31:23] NaiveAssociation -- processed 20% of features. INFO [2026-01-12 10:31:23] NaiveAssociation -- processed 26.67% of features. INFO [2026-01-12 10:31:23] NaiveAssociation -- processed 33.33% of features. INFO [2026-01-12 10:31:23] NaiveAssociation -- processed 40% of features. INFO [2026-01-12 10:31:23] NaiveAssociation -- processed 46.67% of features. INFO [2026-01-12 10:31:23] NaiveAssociation -- processed 53.33% of features. INFO [2026-01-12 10:31:24] NaiveAssociation -- processed 60% of features. INFO [2026-01-12 10:31:24] NaiveAssociation -- processed 66.67% of features. INFO [2026-01-12 10:31:24] NaiveAssociation -- processed 73.33% of features. INFO [2026-01-12 10:31:24] NaiveAssociation -- processed 80% of features. INFO [2026-01-12 10:31:24] NaiveAssociation -- processed 86.67% of features. INFO [2026-01-12 10:31:24] NaiveAssociation -- processed 93.33% of features. INFO [2026-01-12 10:31:24] NaiveAssociation -- processed 100% of features. INFO [2026-01-12 10:31:24] NaiveAssociation -- processed 100% of features. starting worker pid=109204 on localhost:11997 at 10:31:24.426 INFO [2026-01-12 10:32:24] Deconfounding -- processed 6.67% of features. INFO [2026-01-12 10:32:34] Deconfounding -- processed 13.33% of features. INFO [2026-01-12 10:32:57] Deconfounding -- processed 20% of features. INFO [2026-01-12 10:32:57] Deconfounding -- processed 26.67% of features. INFO [2026-01-12 10:32:58] Deconfounding -- processed 33.33% of features. INFO [2026-01-12 10:33:19] Deconfounding -- processed 40% of features. INFO [2026-01-12 10:33:43] Deconfounding -- processed 46.67% of features. INFO [2026-01-12 10:33:43] Deconfounding -- processed 53.33% of features. INFO [2026-01-12 10:33:44] Deconfounding -- processed 60% of features. INFO [2026-01-12 10:33:45] Deconfounding -- processed 66.67% of features. INFO [2026-01-12 10:34:08] Deconfounding -- processed 73.33% of features. INFO [2026-01-12 10:34:08] Deconfounding -- processed 80% of features. INFO [2026-01-12 10:34:08] Deconfounding -- processed 86.67% of features. INFO [2026-01-12 10:34:20] Deconfounding -- processed 93.33% of features. INFO [2026-01-12 10:34:20] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:34:20] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:34:20] Removing 'confounded confounders' from status labels. Set noConfConfs = FALSE to keep them. INFO [2026-01-12 10:34:20] MetadecondoundR run completed successfully! ERROR [2026-01-12 10:34:20] Necessary argument "metaMat" missing. ERROR [2026-01-12 10:34:20] Necessary argument "featureMat" missing. ERROR [2026-01-12 10:34:20] featureMat and metaMat don't have same number of rows. ERROR [2026-01-12 10:34:20] rownames of featureMat and metaMat don't have same order. INFO [2026-01-12 10:34:20] ### ### Deconfounding run started WARN [2026-01-12 10:34:20] 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 [2026-01-12 10:34:20] Elements of deconfT/deconfF are not present in colnames of metaMat. INFO [2026-01-12 10:34:20] Check identical spelling of variable names in deconfT/deconfF and metaMat ERROR [2026-01-12 10:34:20] Some elements of deconfT and deconfF seem to be identical. ERROR [2026-01-12 10:34:20] rawCounts and logistic can not be both set to TRUE! ERROR [2026-01-12 10:34:20] QValues and/or DValues argument is supplied but seems to be empty (NULL). ERROR [2026-01-12 10:34:20] randomVar does not need to be supplied as list anymore, please change to new syntax. ERROR [2026-01-12 10:34:20] 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 [2026-01-12 10:34:20] Non-numeric columns detected in featureMat. INFO [2026-01-12 10:34:20] ### ### Deconfounding run started WARN [2026-01-12 10:34:20] 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 [2026-01-12 10:34:20] Computing in serial mode. Set nnodes > 1 do to switch to faster parallel processing. INFO [2026-01-12 10:34:20] Checking robustness of data for covariates INFO [2026-01-12 10:34:20] Computation of naive associations started. starting worker pid=92044 on localhost:11997 at 10:34:21.026 INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 2% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 4% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 6% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 8% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 10% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 12% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 14% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 16% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 18% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 20% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 22% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 24% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 26% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 28% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 30% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 32% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 34% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 36% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 38% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 40% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 42% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 44% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 46% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 48% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 50% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 52% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 54% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 56% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 58% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 60% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 62% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 64% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 66% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 68% of features. INFO [2026-01-12 10:34:21] NaiveAssociation -- processed 70% of features. INFO [2026-01-12 10:34:22] NaiveAssociation -- processed 72% of features. INFO [2026-01-12 10:34:22] NaiveAssociation -- processed 74% of features. INFO [2026-01-12 10:34:22] NaiveAssociation -- processed 76% of features. INFO [2026-01-12 10:34:22] NaiveAssociation -- processed 78% of features. INFO [2026-01-12 10:34:22] NaiveAssociation -- processed 80% of features. INFO [2026-01-12 10:34:22] NaiveAssociation -- processed 82% of features. INFO [2026-01-12 10:34:22] NaiveAssociation -- processed 84% of features. INFO [2026-01-12 10:34:22] NaiveAssociation -- processed 86% of features. INFO [2026-01-12 10:34:22] NaiveAssociation -- processed 88% of features. INFO [2026-01-12 10:34:22] NaiveAssociation -- processed 90% of features. INFO [2026-01-12 10:34:22] NaiveAssociation -- processed 92% of features. INFO [2026-01-12 10:34:22] NaiveAssociation -- processed 94% of features. INFO [2026-01-12 10:34:22] NaiveAssociation -- processed 96% of features. INFO [2026-01-12 10:34:22] NaiveAssociation -- processed 98% of features. INFO [2026-01-12 10:34:22] NaiveAssociation -- processed 100% of features. INFO [2026-01-12 10:34:22] NaiveAssociation -- processed 100% of features. starting worker pid=50640 on localhost:11997 at 10:34:22.595 INFO [2026-01-12 10:34:22] Deconfounding -- processed 2% of features. INFO [2026-01-12 10:34:22] Deconfounding -- processed 4% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 6% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 8% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 10% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 12% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 14% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 16% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 18% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 20% of features. WARN [2026-01-12 10:34:23] lrt: MS0038 Status Metformin -- forward linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0. WARN [2026-01-12 10:34:23] lrt: MS0038 Metformin Status -- reverse linear model is < PHS_cutoff, but confidence intervall for Status is spanning 0. INFO [2026-01-12 10:34:23] Deconfounding -- processed 22% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 24% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 26% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 28% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 30% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 32% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 34% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 36% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 38% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 40% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 42% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 44% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 46% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 48% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 50% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 52% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 54% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 56% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 58% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 60% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 62% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 64% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 66% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 68% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 70% of features. INFO [2026-01-12 10:34:23] Deconfounding -- processed 72% of features. INFO [2026-01-12 10:34:24] Deconfounding -- processed 74% of features. INFO [2026-01-12 10:34:24] Deconfounding -- processed 76% of features. INFO [2026-01-12 10:34:24] Deconfounding -- processed 78% of features. INFO [2026-01-12 10:34:24] Deconfounding -- processed 80% of features. INFO [2026-01-12 10:34:24] Deconfounding -- processed 82% of features. INFO [2026-01-12 10:34:24] Deconfounding -- processed 84% of features. INFO [2026-01-12 10:34:24] Deconfounding -- processed 86% of features. INFO [2026-01-12 10:34:24] Deconfounding -- processed 88% of features. INFO [2026-01-12 10:34:24] Deconfounding -- processed 90% of features. INFO [2026-01-12 10:34:24] Deconfounding -- processed 92% of features. INFO [2026-01-12 10:34:24] Deconfounding -- processed 94% of features. INFO [2026-01-12 10:34:24] Deconfounding -- processed 96% of features. INFO [2026-01-12 10:34:24] Deconfounding -- processed 98% of features. INFO [2026-01-12 10:34:24] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:34:24] Deconfounding -- processed 100% of features. INFO [2026-01-12 10:34:24] Removing 'confounded confounders' from status labels. Set noConfConfs = FALSE to keep them. INFO [2026-01-12 10:34:24] MetadecondoundR run completed successfully! [ FAIL 0 | WARN 0 | SKIP 0 | PASS 68 ] > > proc.time() user system elapsed 448.75 5.40 483.78