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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings EpiCompare_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/EpiCompare.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘EpiCompare/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EpiCompare’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘EpiCompare’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
tss_plot              39.892  7.795  47.690
compute_corr          11.171  2.432  10.742
rebin_peaks            7.438  1.879   4.771
plot_corr              7.084  1.653   7.153
plot_chromHMM          4.945  0.901   5.695
plot_precision_recall  4.200  1.073   3.045
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘EpiCompare.Rmd’ using ‘UTF-8’... OK
  ‘docker.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL EpiCompare
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘EpiCompare’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package keeps a record of temporary installation path
* DONE (EpiCompare)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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.

> library(testthat)
> library(EpiCompare)

Warning message:
replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' 
> 
> test_check("EpiCompare")
[1] "Done in 1.261 min."
All outputs saved to: /tmp/RtmpciFVXj/EpiCompare_test
[1] "Done in 0.085 min."
All outputs saved to: /tmp/RtmpciFVXj/EpiCompare_test
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Removing non-standard chromosomes.
Computing consensus peaks for group: Imperial 
 - 2 files 
 - 1,670-2,707 peaks each
Identified 1,325 consensus peaks from 2 peak files
Computing consensus peaks for group: ENCODE 
 - 1 files 
 - 5,142-5,142 peaks each
WARNING: Cannot compute consensus peaks when group has <2 peak files. Returning original GRanges object instead.
Done computing consensus peaks in 0 min.
Loading required namespace: consensusSeekeR
Removing non-standard chromosomes.
Computing consensus peaks for group: Imperial 
 - 2 files 
 - 1,670-2,707 peaks each
Loading required namespace: BSgenome.Hsapiens.UCSC.hg19
Identified 2,982 consensus peaks from 2 peak files
Computing consensus peaks for group: ENCODE 
 - 1 files 
 - 5,142-5,142 peaks each
WARNING: Cannot compute consensus peaks when group has <2 peak files. Returning original GRanges object instead.
Done computing consensus peaks in 0.36 min.
Standardising peak files in 6,659 bins of 5e+05 bp.
Merging data into matrix.
Binned matrix size: 6,659 x 3
Matrix sparsity: 0.9526
Calculating correlation matrix.
Done computing correlations in 2 seconds.
Standardising peak files in 32,488 bins of 1e+05 bp.
Merging data into matrix.
Binned matrix size: 32,488 x 3
Matrix sparsity: 0.974
Calculating correlation matrix.
Done computing correlations in 2 seconds.
Standardising peak files in 323,636 bins of 1e+04 bp.
Merging data into matrix.
Binned matrix size: 323,636 x 3
Matrix sparsity: 0.9936
Calculating correlation matrix.
Done computing correlations in 3 seconds.
Standardising peak files in 647,114 bins of 5,000 bp.
Merging data into matrix.
Binned matrix size: 647,114 x 3
Matrix sparsity: 0.996
Calculating correlation matrix.
Done computing correlations in 6 seconds.
Loading required namespace: plyranges
Writing ==> /tmp/RtmpciFVXj/processed_results/encode_H3K27ac.narrowPeaks.bed
Writing ==> /tmp/RtmpciFVXj/processed_results/CnT_H3K27ac.narrowPeaks.bed
Writing ==> /tmp/RtmpciFVXj/processed_results/CnR_H3K27ac.narrowPeaks.bed
Searching for *.narrowPeaks.bed$ files...
3 matching files identified.
Constructing file names.
Importing files.
Reading narrowPeaks
Reading narrowPeaks
Reading narrowPeaks
3 files retrieved.
Searching for peaks.narrow files...
3 matching files identified.
Constructing file names.
Returning paths.
Searching for peaks.narrow files...
0 matching files identified. Returning NULL.
--- Running peak_info() ---
Done.
--- Running fragment_info() ---
Done.
--- Running width_boxplot() ---
Done.
Writing ==> /tmp/RtmpciFVXj/processed_results/encode_H3K27ac.narrowPeaks.bed
Preparing chain file.
snapshotDate(): 2022-10-31
loading from cache
require("rtracklayer")
Performing liftover:  hg19  -->  hg38
Removing non-standard chromosomes.
Preparing chain file.
snapshotDate(): 2022-10-31
Preparing chain file.
snapshotDate(): 2022-10-31
loading from cache
Performing liftover:  hg38  -->  hg19
Removing non-standard chromosomes.
loading from cache
Performing liftover:  hg19  -->  mm9
Removing non-standard chromosomes.
[1] "Done in 0.051 min."
All outputs saved to: /tmp/RtmpciFVXj/EpiCompare_test
[1] "Done in 0.044 min."
All outputs saved to: /tmp/RtmpciFVXj/EpiCompare_test
[1] "Done in 0.05 min."
All outputs saved to: /tmp/RtmpciFVXj/EpiCompare_test
--- Running overlap_heatmap() ---
Done.
--- Running overlap_heatmap() ---
Done.
--- Running overlap_upset_plot() ---
Done.
--- Running overlap_stat_plot() ---
Preparing reference.
Extracting GRanges object from list.
Done.
Standardising peak files in 3,235,000 bins of 1,000 bp.
Merging data into matrix.
Binned matrix size: 3,235,000 x 3
Matrix sparsity: 0.9983
Calculating correlation matrix.
Done computing correlations in 19 seconds.
Threshold=0: Filtering peaks
Threshold=0.1: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.2: Filtering peaks
Threshold=0.3: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.4: Filtering peaks
Threshold=0.5: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.6: Filtering peaks
Threshold=0.7: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.8: Filtering peaks
Threshold=0.9: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
WARNING: 'CnT_missing' missing threshold col, will be excluded from precision-recall calculations.
Standardising peak files in 647,114 bins of 5,000 bp.
Merging data into matrix.
Converting to sparse matrix.
Binned matrix size: 647,114 x 2
Matrix sparsity: 0.9968
WARNING: 'CnT_missing' missing threshold col, will be excluded from precision-recall calculations.
Standardising peak files in 416,959 bins of 5,000 bp.
Merging data into matrix.
Converting to sparse matrix.
Binned matrix size: 416,959 x 2
Matrix sparsity: 0.995
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 86 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
183.450  22.939 206.960