############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ramwas ### ############################################################################## ############################################################################## * checking for file ‘ramwas/DESCRIPTION’ ... OK * preparing ‘ramwas’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘RW1_intro.Rmd’ using rmarkdown Thu Jul 7 03:07:53 2022, Start ramwas0createArtificialData() call Thu Jul 7 03:07:53 2022, Generating 25000 CpG locations Thu Jul 7 03:07:53 2022, Saving CpG locations in: /tmp/RtmpUvdDFh/simulated_project/Simulated_chromosome.rds Thu Jul 7 03:07:53 2022, Generating fragment size distribution Thu Jul 7 03:07:53 2022, Generating covariates Thu Jul 7 03:07:53 2022, Savings covariates in: /tmp/RtmpUvdDFh/simulated_project/covariates.txt Thu Jul 7 03:07:53 2022, Savings BAM list in: /tmp/RtmpUvdDFh/simulated_project/bam_list.txt Thu Jul 7 03:07:53 2022, Start generating BAM files in: /tmp/RtmpUvdDFh/simulated_project/bams Thu Jul 7 03:08:13 2022, Done generating BAM files in: /tmp/RtmpUvdDFh/simulated_project/bams Thu Jul 7 03:08:13 2022, Start ramwas1scanBams() call Thu Jul 7 03:08:34 2022, Done ramwas1scanBams() call Working in: /tmp/RtmpUvdDFh/simulated_project/qc Load BAM QC info Saving QC info by BAM Saving plots score Saving plots score_before_filter Saving plots edit_distance Saving plots edit_distance_before_filter Saving plots matched_length Saving plots matched_length_before_filter Saving plots isolated_distance Saving plots coverage_by_density Saving QC info by BAMs in bam2sample Saving plots score Saving plots score_before_filter Saving plots edit_distance Saving plots edit_distance_before_filter Saving plots matched_length Saving plots matched_length_before_filter Saving plots isolated_distance Saving plots coverage_by_density Saving QC info by SAMPLE Saving plots score Saving plots score_before_filter Saving plots edit_distance Saving plots edit_distance_before_filter Saving plots matched_length Saving plots matched_length_before_filter Saving plots isolated_distance Saving plots coverage_by_density Saving QC info TOTAL (all BAMs in bam2sample) Saving plots score Saving plots score_before_filter Saving plots edit_distance Saving plots edit_distance_before_filter Saving plots matched_length Saving plots matched_length_before_filter Saving plots isolated_distance Saving plots coverage_by_density Using the 20 samples in the covariate file. Checking if all required Rbam files present All required Rbam files present are present. Working in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20 Thu Jul 7 03:08:36 2022, Start ramwas3normalizedCoverage() Thu Jul 7 03:08:36 2022, Creating 1 file matrices for raw scores at: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/temp Thu Jul 7 03:08:36 2022, Calculating raw coverage Thu Jul 7 03:08:48 2022, Done calculating raw coverage Thu Jul 7 03:08:48 2022, Transposing score matrices and filtering CpGs by score Thu Jul 7 03:08:48 2022, Process 007751, Start transposing slice: 001 Thu Jul 7 03:08:49 2022, Process 007751, Done transposing slice: 001 Thu Jul 7 03:08:49 2022, Done transposing score matrices, filtering CpGs Thu Jul 7 03:08:49 2022, Saving locations for CpGs which passed the filter Thu Jul 7 03:08:49 2022, Gathering sample sums from 1 slices Thu Jul 7 03:08:49 2022, Normalizing coverage and saving in one matrix Thu Jul 7 03:08:49 2022, Process 007751, Start normalizing slice: 001 Thu Jul 7 03:08:49 2022, Process 007751, Done normalizing slice: 001 Thu Jul 7 03:08:49 2022, Done Normalizing coverage matrix. Thu Jul 7 03:08:49 2022, Done ramwas3normalizedCoverage() call Thu Jul 7 03:08:49 2022, Start ramwas4PCA() call Working in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/PCA_00_cvrts Thu Jul 7 03:08:49 2022, Calculating covariance matrix Thu Jul 7 03:08:49 2022, Process 007751, Job 00, Start PCA, CpG range 1-23546 Thu Jul 7 03:08:49 2022, Process 007751, Job 00, Processing slice: 001 of 1 Thu Jul 7 03:08:49 2022, Process 007751, Job 00, Done PCA, CpG range 1-23546 Thu Jul 7 03:08:50 2022, Done calculating covariance matrix Thu Jul 7 03:08:50 2022, Saving covariance matrix Thu Jul 7 03:08:50 2022, Performing Eigenvalue Decomposition Thu Jul 7 03:08:50 2022, Saving Eigenvalue Decomposition Thu Jul 7 03:08:50 2022, Start postPCAprocessing() call Thu Jul 7 03:08:50 2022, Saving PCA plots in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/PCA_00_cvrts/PC_plot_covariates_removed.pdf Thu Jul 7 03:08:50 2022, Saving PC values and vectors Thu Jul 7 03:08:50 2022, Saving PC vs. covariates associations Thu Jul 7 03:08:50 2022, Done postPCAprocessing() call Thu Jul 7 03:08:50 2022, Done ramwas4PCA() call Thu Jul 7 03:08:51 2022, Start ramwas5MWAS() call Working in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/PCA_00_cvrts/Testing_age_0_PCs Thu Jul 7 03:08:51 2022, Creating output matrix Thu Jul 7 03:08:51 2022, Start Association Analysis Thu Jul 7 03:08:51 2022, Process 007751, Job 00, Start MWAS, CpG range 1-23546 Thu Jul 7 03:08:51 2022, Process 007751, Job 00, Processing slice: 001 of 1 Thu Jul 7 03:08:51 2022, Process 007751, Job 00, Done MWAS, CpG range 1-23546 Thu Jul 7 03:08:51 2022, Done Association Analysis Thu Jul 7 03:08:51 2022, Calculating FDR (q-values) Thu Jul 7 03:08:51 2022, Creating QQ-plot Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Thu Jul 7 03:08:51 2022, Creating QQ-plot and Manhattan plot pair Working in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/PCA_00_cvrts/Testing_age_0_PCs Loading MWAS results Finding top MWAS hits Saving top MWAS hits Thu Jul 7 03:08:53 2022, Done ramwas5MWAS() call Thu Jul 7 03:08:56 2022, Start ramwas7ArunMWASes() call Working in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/PCA_00_cvrts/Testing_age_0_PCs/CV_05_folds Thu Jul 7 03:08:56 2022, Start MWAS for fold 01 of 5 Thu Jul 7 03:08:56 2022, Start ramwas5MWAS() call Working in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/PCA_00_cvrts/Testing_age_0_PCs/CV_05_folds/fold_01 Thu Jul 7 03:08:56 2022, Removing observations with missing outcome Thu Jul 7 03:08:56 2022, Creating output matrix Thu Jul 7 03:08:56 2022, Start Association Analysis Thu Jul 7 03:08:56 2022, Process 007751, Job 00, Start MWAS, CpG range 1-23546 Thu Jul 7 03:08:56 2022, Process 007751, Job 00, Processing slice: 001 of 1 Thu Jul 7 03:08:56 2022, Process 007751, Job 00, Done MWAS, CpG range 1-23546 Thu Jul 7 03:08:56 2022, Done Association Analysis Thu Jul 7 03:08:56 2022, Calculating FDR (q-values) Thu Jul 7 03:08:56 2022, Creating QQ-plot Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Thu Jul 7 03:08:56 2022, Creating QQ-plot and Manhattan plot pair Working in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/PCA_00_cvrts/Testing_age_0_PCs/CV_05_folds/fold_01 Loading MWAS results Finding top MWAS hits Saving top MWAS hits Thu Jul 7 03:08:58 2022, Done ramwas5MWAS() call Thu Jul 7 03:08:58 2022, Start MWAS for fold 02 of 5 Thu Jul 7 03:08:58 2022, Start ramwas5MWAS() call Working in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/PCA_00_cvrts/Testing_age_0_PCs/CV_05_folds/fold_02 Thu Jul 7 03:08:58 2022, Removing observations with missing outcome Thu Jul 7 03:08:58 2022, Creating output matrix Thu Jul 7 03:08:58 2022, Start Association Analysis Thu Jul 7 03:08:58 2022, Process 007751, Job 00, Start MWAS, CpG range 1-23546 Thu Jul 7 03:08:58 2022, Process 007751, Job 00, Processing slice: 001 of 1 Thu Jul 7 03:08:58 2022, Process 007751, Job 00, Done MWAS, CpG range 1-23546 Thu Jul 7 03:08:58 2022, Done Association Analysis Thu Jul 7 03:08:58 2022, Calculating FDR (q-values) Thu Jul 7 03:08:58 2022, Creating QQ-plot Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Thu Jul 7 03:08:58 2022, Creating QQ-plot and Manhattan plot pair Working in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/PCA_00_cvrts/Testing_age_0_PCs/CV_05_folds/fold_02 Loading MWAS results Finding top MWAS hits Saving top MWAS hits Thu Jul 7 03:09:00 2022, Done ramwas5MWAS() call Thu Jul 7 03:09:00 2022, Start MWAS for fold 03 of 5 Thu Jul 7 03:09:00 2022, Start ramwas5MWAS() call Working in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/PCA_00_cvrts/Testing_age_0_PCs/CV_05_folds/fold_03 Thu Jul 7 03:09:00 2022, Removing observations with missing outcome Thu Jul 7 03:09:00 2022, Creating output matrix Thu Jul 7 03:09:00 2022, Start Association Analysis Thu Jul 7 03:09:00 2022, Process 007751, Job 00, Start MWAS, CpG range 1-23546 Thu Jul 7 03:09:00 2022, Process 007751, Job 00, Processing slice: 001 of 1 Thu Jul 7 03:09:00 2022, Process 007751, Job 00, Done MWAS, CpG range 1-23546 Thu Jul 7 03:09:00 2022, Done Association Analysis Thu Jul 7 03:09:00 2022, Calculating FDR (q-values) Thu Jul 7 03:09:00 2022, Creating QQ-plot Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Thu Jul 7 03:09:00 2022, Creating QQ-plot and Manhattan plot pair Working in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/PCA_00_cvrts/Testing_age_0_PCs/CV_05_folds/fold_03 Loading MWAS results Finding top MWAS hits Saving top MWAS hits Thu Jul 7 03:09:02 2022, Done ramwas5MWAS() call Thu Jul 7 03:09:02 2022, Start MWAS for fold 04 of 5 Thu Jul 7 03:09:02 2022, Start ramwas5MWAS() call Working in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/PCA_00_cvrts/Testing_age_0_PCs/CV_05_folds/fold_04 Thu Jul 7 03:09:02 2022, Removing observations with missing outcome Thu Jul 7 03:09:02 2022, Creating output matrix Thu Jul 7 03:09:02 2022, Start Association Analysis Thu Jul 7 03:09:02 2022, Process 007751, Job 00, Start MWAS, CpG range 1-23546 Thu Jul 7 03:09:02 2022, Process 007751, Job 00, Processing slice: 001 of 1 Thu Jul 7 03:09:02 2022, Process 007751, Job 00, Done MWAS, CpG range 1-23546 Thu Jul 7 03:09:02 2022, Done Association Analysis Thu Jul 7 03:09:02 2022, Calculating FDR (q-values) Thu Jul 7 03:09:02 2022, Creating QQ-plot Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Thu Jul 7 03:09:03 2022, Creating QQ-plot and Manhattan plot pair Working in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/PCA_00_cvrts/Testing_age_0_PCs/CV_05_folds/fold_04 Loading MWAS results Finding top MWAS hits Saving top MWAS hits Thu Jul 7 03:09:05 2022, Done ramwas5MWAS() call Thu Jul 7 03:09:05 2022, Start MWAS for fold 05 of 5 Thu Jul 7 03:09:05 2022, Start ramwas5MWAS() call Working in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/PCA_00_cvrts/Testing_age_0_PCs/CV_05_folds/fold_05 Thu Jul 7 03:09:05 2022, Removing observations with missing outcome Thu Jul 7 03:09:05 2022, Creating output matrix Thu Jul 7 03:09:05 2022, Start Association Analysis Thu Jul 7 03:09:05 2022, Process 007751, Job 00, Start MWAS, CpG range 1-23546 Thu Jul 7 03:09:05 2022, Process 007751, Job 00, Processing slice: 001 of 1 Thu Jul 7 03:09:05 2022, Process 007751, Job 00, Done MWAS, CpG range 1-23546 Thu Jul 7 03:09:05 2022, Done Association Analysis Thu Jul 7 03:09:05 2022, Calculating FDR (q-values) Thu Jul 7 03:09:05 2022, Creating QQ-plot Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Thu Jul 7 03:09:05 2022, Creating QQ-plot and Manhattan plot pair Working in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/PCA_00_cvrts/Testing_age_0_PCs/CV_05_folds/fold_05 Loading MWAS results Finding top MWAS hits Saving top MWAS hits Thu Jul 7 03:09:07 2022, Done ramwas5MWAS() call Thu Jul 7 03:09:07 2022, Start ramwas7BrunElasticNet() call Thu Jul 7 03:09:07 2022, Applying Elasting Net to 5 top CpGs Thu Jul 7 03:09:07 2022, Processing fold 01 of 5 Thu Jul 7 03:09:09 2022, Processing fold 02 of 5 Thu Jul 7 03:09:10 2022, Processing fold 03 of 5 Thu Jul 7 03:09:12 2022, Processing fold 04 of 5 Thu Jul 7 03:09:13 2022, Processing fold 05 of 5 Thu Jul 7 03:09:14 2022, Saving Cross Validation Predictions and Plots Thu Jul 7 03:09:14 2022, Applying Elasting Net to 10 top CpGs Thu Jul 7 03:09:14 2022, Processing fold 01 of 5 Thu Jul 7 03:09:16 2022, Processing fold 02 of 5 Thu Jul 7 03:09:17 2022, Processing fold 03 of 5 Thu Jul 7 03:09:18 2022, Processing fold 04 of 5 Thu Jul 7 03:09:20 2022, Processing fold 05 of 5 Thu Jul 7 03:09:21 2022, Saving Cross Validation Predictions and Plots Thu Jul 7 03:09:21 2022, Applying Elasting Net to 50 top CpGs Thu Jul 7 03:09:21 2022, Processing fold 01 of 5 Thu Jul 7 03:09:22 2022, Processing fold 02 of 5 Thu Jul 7 03:09:24 2022, Processing fold 03 of 5 Thu Jul 7 03:09:25 2022, Processing fold 04 of 5 Thu Jul 7 03:09:26 2022, Processing fold 05 of 5 Thu Jul 7 03:09:27 2022, Saving Cross Validation Predictions and Plots Thu Jul 7 03:09:27 2022, Applying Elasting Net to 100 top CpGs Thu Jul 7 03:09:27 2022, Processing fold 01 of 5 Thu Jul 7 03:09:29 2022, Processing fold 02 of 5 Thu Jul 7 03:09:30 2022, Processing fold 03 of 5 Thu Jul 7 03:09:32 2022, Processing fold 04 of 5 Thu Jul 7 03:09:33 2022, Processing fold 05 of 5 Thu Jul 7 03:09:34 2022, Saving Cross Validation Predictions and Plots Thu Jul 7 03:09:34 2022, Applying Elasting Net to 500 top CpGs Thu Jul 7 03:09:34 2022, Processing fold 01 of 5 Thu Jul 7 03:09:36 2022, Processing fold 02 of 5 Thu Jul 7 03:09:37 2022, Processing fold 03 of 5 Thu Jul 7 03:09:39 2022, Processing fold 04 of 5 Thu Jul 7 03:09:40 2022, Processing fold 05 of 5 Thu Jul 7 03:09:41 2022, Saving Cross Validation Predictions and Plots Thu Jul 7 03:09:41 2022, Applying Elasting Net to 1000 top CpGs Thu Jul 7 03:09:41 2022, Processing fold 01 of 5 Thu Jul 7 03:09:43 2022, Processing fold 02 of 5 Thu Jul 7 03:09:44 2022, Processing fold 03 of 5 Thu Jul 7 03:09:46 2022, Processing fold 04 of 5 Thu Jul 7 03:09:48 2022, Processing fold 05 of 5 Thu Jul 7 03:09:49 2022, Saving Cross Validation Predictions and Plots Thu Jul 7 03:09:49 2022, Applying Elasting Net to 2000 top CpGs Thu Jul 7 03:09:49 2022, Processing fold 01 of 5 Thu Jul 7 03:09:51 2022, Processing fold 02 of 5 Thu Jul 7 03:09:52 2022, Processing fold 03 of 5 Thu Jul 7 03:09:54 2022, Processing fold 04 of 5 Thu Jul 7 03:09:56 2022, Processing fold 05 of 5 Thu Jul 7 03:09:58 2022, Saving Cross Validation Predictions and Plots Thu Jul 7 03:09:58 2022, Done ramwas7BrunElasticNet() call Working in: /tmp/RtmpUvdDFh/simulated_project/coverage_norm_20/PCA_00_cvrts/Testing_age_0_PCs/CV_05_folds --- finished re-building ‘RW1_intro.Rmd’ --- re-building ‘RW2_CpG_sets.Rmd’ using rmarkdown Quitting from lines 87-89 (RW2_CpG_sets.Rmd) Error: processing vignette 'RW2_CpG_sets.Rmd' failed with diagnostics: there is no package called 'BSgenome.Ecoli.NCBI.20080805' --- failed re-building ‘RW2_CpG_sets.Rmd’ --- re-building ‘RW3_BAM_QCs.Rmd’ using rmarkdown --- finished re-building ‘RW3_BAM_QCs.Rmd’ --- re-building ‘RW4_SNPs.Rmd’ using rmarkdown Working in: /tmp/RtmpUvdDFh/simulated_matrix_data/Testing_wSNPs_sex_1cvrts_0PCs Preparing for MWAS with SNPs Matching samples in covariates and data matrix Preparing covariates (splitting dummies, orthonormalizing) Creating output matrix Running MWAS Slice 1 of 1 Calculating FDR (q-values) Creating QQ-plot Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Working in: /tmp/RtmpUvdDFh/simulated_matrix_data/Testing_wSNPs_sex_1cvrts_0PCs Loading MWAS results Loading CpG locations Finding top MWAS hits Saving top MWAS hits Thu Jul 7 03:10:17 2022, Start ramwas5MWAS() call Working in: /tmp/RtmpUvdDFh/simulated_matrix_data/PCA_01_cvrts_f80b52d4/Testing_sex_0_PCs Thu Jul 7 03:10:17 2022, Creating output matrix Thu Jul 7 03:10:17 2022, Start Association Analysis Thu Jul 7 03:10:29 2022, Done Association Analysis Thu Jul 7 03:10:29 2022, Calculating FDR (q-values) Thu Jul 7 03:10:29 2022, Creating QQ-plot Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Thu Jul 7 03:10:29 2022, Creating QQ-plot and Manhattan plot pair Working in: /tmp/RtmpUvdDFh/simulated_matrix_data/PCA_01_cvrts_f80b52d4/Testing_sex_0_PCs Loading MWAS results Finding top MWAS hits Saving top MWAS hits Thu Jul 7 03:10:32 2022, Done ramwas5MWAS() call --- finished re-building ‘RW4_SNPs.Rmd’ --- re-building ‘RW5a_matrix.Rmd’ using rmarkdown --- finished re-building ‘RW5a_matrix.Rmd’ --- re-building ‘RW5c_matrix.Rmd’ using rmarkdown Thu Jul 7 03:10:38 2022, Start ramwas4PCA() call Working in: /tmp/RtmpUvdDFh/simulated_matrix_data/PCA_00_cvrts Thu Jul 7 03:10:38 2022, Calculating covariance matrix Thu Jul 7 03:10:55 2022, Done calculating covariance matrix Thu Jul 7 03:10:55 2022, Saving covariance matrix Thu Jul 7 03:10:55 2022, Performing Eigenvalue Decomposition Thu Jul 7 03:10:55 2022, Saving Eigenvalue Decomposition Thu Jul 7 03:10:55 2022, Start postPCAprocessing() call Thu Jul 7 03:10:55 2022, Saving PCA plots in: /tmp/RtmpUvdDFh/simulated_matrix_data/PCA_00_cvrts/PC_plot_covariates_removed.pdf Thu Jul 7 03:10:55 2022, Saving PC values and vectors Thu Jul 7 03:10:55 2022, Saving PC vs. covariates associations Thu Jul 7 03:10:55 2022, Done postPCAprocessing() call Thu Jul 7 03:10:55 2022, Done ramwas4PCA() call Thu Jul 7 03:10:57 2022, Start ramwas4PCA() call Working in: /tmp/RtmpUvdDFh/simulated_matrix_data/PCA_01_cvrts_f80b52d4 Thu Jul 7 03:10:57 2022, Calculating covariance matrix Thu Jul 7 03:11:13 2022, Done calculating covariance matrix Thu Jul 7 03:11:13 2022, Saving covariance matrix Thu Jul 7 03:11:13 2022, Performing Eigenvalue Decomposition Thu Jul 7 03:11:13 2022, Saving Eigenvalue Decomposition Thu Jul 7 03:11:13 2022, Start postPCAprocessing() call Thu Jul 7 03:11:13 2022, Saving PCA plots in: /tmp/RtmpUvdDFh/simulated_matrix_data/PCA_01_cvrts_f80b52d4/PC_plot_covariates_removed.pdf Thu Jul 7 03:11:13 2022, Saving PC values and vectors Thu Jul 7 03:11:13 2022, Saving PC vs. covariates associations Thu Jul 7 03:11:13 2022, Done postPCAprocessing() call Thu Jul 7 03:11:13 2022, Done ramwas4PCA() call Thu Jul 7 03:11:13 2022, Start ramwas5MWAS() call Working in: /tmp/RtmpUvdDFh/simulated_matrix_data/PCA_01_cvrts_f80b52d4/Testing_sex_0_PCs Thu Jul 7 03:11:13 2022, Creating output matrix Thu Jul 7 03:11:13 2022, Start Association Analysis Thu Jul 7 03:11:25 2022, Done Association Analysis Thu Jul 7 03:11:25 2022, Calculating FDR (q-values) Thu Jul 7 03:11:25 2022, Creating QQ-plot Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : font metrics unknown for Unicode character U+2013 Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <80> Warning in title(...) : conversion failure on '–' in 'mbcsToSbcs': dot substituted for <93> Thu Jul 7 03:11:25 2022, Creating QQ-plot and Manhattan plot pair Working in: /tmp/RtmpUvdDFh/simulated_matrix_data/PCA_01_cvrts_f80b52d4/Testing_sex_0_PCs Loading MWAS results Finding top MWAS hits Saving top MWAS hits Thu Jul 7 03:11:28 2022, Done ramwas5MWAS() call --- finished re-building ‘RW5c_matrix.Rmd’ --- re-building ‘RW6_param.Rmd’ using rmarkdown --- finished re-building ‘RW6_param.Rmd’ SUMMARY: processing the following file failed: ‘RW2_CpG_sets.Rmd’ Error: Vignette re-building failed. Execution halted