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This page was generated on 2022-07-07 11:11:48 -0400 (Thu, 07 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4148
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4160
kjohnsonmacOS 12.4 Montereyarm644.2.0 Patched (2022-06-09 r82473) -- "Vigorous Calisthenics" 3115
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD results for ramwas on kjohnson


To the developers/maintainers of the ramwas package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ramwas.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
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raw results

Package 1550/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ramwas 1.21.0  (landing page)
Andrey A Shabalin
Snapshot Date: 2022-07-06 14:00:06 -0400 (Wed, 06 Jul 2022)
git_url: https://git.bioconductor.org/packages/ramwas
git_branch: master
git_last_commit: e5462e3
git_last_commit_date: 2022-04-26 11:38:08 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnsonmacOS 12.4 Monterey / arm64  OK    ERROR  skippedskipped

Summary

Package: ramwas
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ramwas
StartedAt: 2022-07-07 03:07:04 -0400 (Thu, 07 Jul 2022)
EndedAt: 2022-07-07 03:11:32 -0400 (Thu, 07 Jul 2022)
EllapsedTime: 268.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### 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
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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
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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
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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
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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
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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
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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
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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
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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
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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