##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings EpiCompare_1.6.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/EpiCompare.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘EpiCompare/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EpiCompare’ version ‘1.6.7’
* 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
plot_enrichment            37.672  2.821  47.958
plot_ChIPseeker_annotation 20.254  1.261  21.515
EpiCompare                  9.473  1.172  10.700
rebin_peaks                 7.463  2.147   4.359
plot_precision_recall       6.673  1.662   4.724
predict_precision_recall    6.172  1.854   3.805
plot_corr                   5.600  1.567   5.521
plot_chromHMM               4.887  0.730   9.872
* 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’... failed
  ‘example_report.Rmd’ using ‘UTF-8’... OK
 ERROR
Errors in running code in vignettes:
when running code in ‘docker.Rmd’
  ...

> pkg <- read.dcf("../DESCRIPTION", fields = "Package")[1]
Warning in read.dcf("../DESCRIPTION", fields = "Package") :
  cannot open compressed file '../DESCRIPTION', probable reason 'No such file or directory'

  When sourcing ‘docker.R’:
Error: cannot open the connection
Execution halted

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/EpiCompare.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL EpiCompare
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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")
All EpiCompare features are being used.
WARNING: precision-recall curves cannot be generated when reference=NULL.


processing file: EpiCompare.Rmd
output file: EpiCompare.knit.md

/usr/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpWxJYrw/t1/EpiCompare.html --lua-filter /home/biocbuild/bbs-3.18-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.18-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /home/biocbuild/bbs-3.18-bioc/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css custom.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpWxJYrw/rmarkdown-str26c43d4b7397f.html --variable code_folding=hide --variable code_menu=1 
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'EpiCompare.knit'

Output created: /tmp/RtmpWxJYrw/t1/EpiCompare.html
[1] "Done in 2.44 min."
All outputs saved to: /tmp/RtmpWxJYrw/t1
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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.
Removing non-standard chromosomes.
Computing consensus peaks for group: Imperial 
 - 2 files 
 - 1,670-2,707 peaks each
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 0.37 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.
Saving correlation results ==> /tmp/RtmpWxJYrw/file26c43d360d52f8.corr.csv.gz
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 3 seconds.
Saving correlation results ==> /tmp/RtmpWxJYrw/file26c43d4de36bb6.corr.csv.gz
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 4 seconds.
Saving correlation results ==> /tmp/RtmpWxJYrw/file26c43d3a33dfb0.corr.csv.gz
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 7 seconds.
Saving correlation results ==> /tmp/RtmpWxJYrw/file26c43d2b42bfee.corr.csv.gz
--- Running fragment_info() ---
Done.
Writing ==> /tmp/RtmpWxJYrw/processed_results/encode_H3K27ac.narrowPeaks.bed
Writing ==> /tmp/RtmpWxJYrw/processed_results/CnT_H3K27ac.narrowPeaks.bed
Writing ==> /tmp/RtmpWxJYrw/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.
Writing ==> /tmp/RtmpWxJYrw/processed_results/encode_H3K27ac.narrowPeaks.bed
Preparing chain file.
loading from cache
require("rtracklayer")
Performing liftover:  hg19  -->  hg38
Removing non-standard chromosomes.
Preparing chain file.
Preparing chain file.
loading from cache
Performing liftover:  hg38  -->  hg19
Removing non-standard chromosomes.
loading from cache
Performing liftover:  hg19  -->  mm9
Removing non-standard chromosomes.
NOTE: The following EpiCompare features are NOT being used: 
 - upset_plot=
 - stat_plot=
 - chromHMM_plot=
 - chipseeker_plot=
 - enrichment_plot=
 - tss_plot=
 - precision_recall_plot=
 - corr_plot=
 - add_download_button=


processing file: EpiCompare.Rmd
output file: EpiCompare.knit.md

/usr/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpWxJYrw/t1/EpiCompare.html --lua-filter /home/biocbuild/bbs-3.18-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.18-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /home/biocbuild/bbs-3.18-bioc/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css custom.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpWxJYrw/rmarkdown-str26c43d23ceaff0.html --variable code_folding=hide --variable code_menu=1 
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'EpiCompare.knit'

Output created: /tmp/RtmpWxJYrw/t1/EpiCompare.html
[1] "Done in 0.12 min."
All outputs saved to: /tmp/RtmpWxJYrw/t1
NOTE: The following EpiCompare features are NOT being used: 
 - upset_plot=
 - stat_plot=
 - chromHMM_plot=
 - chipseeker_plot=
 - enrichment_plot=
 - tss_plot=
 - precision_recall_plot=
 - corr_plot=
 - add_download_button=


processing file: EpiCompare.Rmd
output file: EpiCompare.knit.md

/usr/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpWxJYrw/t2/EpiCompare.html --lua-filter /home/biocbuild/bbs-3.18-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.18-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /home/biocbuild/bbs-3.18-bioc/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css custom.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpWxJYrw/rmarkdown-str26c43d7351c94b.html --variable code_folding=hide --variable code_menu=1 
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'EpiCompare.knit'

Output created: /tmp/RtmpWxJYrw/t2/EpiCompare.html
[1] "Done in 0.13 min."
All outputs saved to: /tmp/RtmpWxJYrw/t2
NOTE: The following EpiCompare features are NOT being used: 
 - upset_plot=
 - stat_plot=
 - chromHMM_plot=
 - chipseeker_plot=
 - enrichment_plot=
 - tss_plot=
 - precision_recall_plot=
 - corr_plot=
 - add_download_button=


processing file: EpiCompare.Rmd
output file: EpiCompare.knit.md

/usr/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpWxJYrw/t3/testthat_example_Apr_15_2024.html --lua-filter /home/biocbuild/bbs-3.18-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.18-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /home/biocbuild/bbs-3.18-bioc/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css custom.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpWxJYrw/rmarkdown-str26c43d2a52c0d.html --variable code_folding=hide --variable code_menu=1 
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'EpiCompare.knit'

Output created: /tmp/RtmpWxJYrw/t3/testthat_example_Apr_15_2024.html
[1] "Done in 0.12 min."
All outputs saved to: /tmp/RtmpWxJYrw/t3
--- Running overlap_heatmap() ---
Warning: fill_diag must =NULL due to a known bug in the package 'heatmaply'.
Genreating precision-recall matrix.
overlap_heatmap(): Done in 3.5s.
--- Running overlap_heatmap() ---
Genreating precision-recall matrix.
overlap_heatmap(): Done in 0.1s.
--- Running overlap_stat_plot() ---
Preparing reference.
Extracting only the first GRanges object from list.
Done.
--- Running overlap_stat_plot() ---
Preparing reference.
Extracting only the first GRanges object from list.
Done.
--- Running peak_info() ---
Done.
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 5 seconds.
Saving correlation results ==> /tmp/RtmpWxJYrw/file26c43d7fa44156.corr.csv.gz
Threshold=0: Filtering peaks
Threshold=0.05: Filtering peaks
Computing precision-recall results.
Threshold=0.1: Filtering peaks
Computing precision-recall results.
Threshold=0.15: Filtering peaks
Computing precision-recall results.
Threshold=0.2: Filtering peaks
Computing precision-recall results.
Threshold=0.25: Filtering peaks
Computing precision-recall results.
Threshold=0.3: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.35: Filtering peaks
Threshold=0.4: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.5: Filtering peaks
Threshold=0.45: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.6: Filtering peaks
Threshold=0.55: Filtering peaks
Computing precision-recall results.
Threshold=0.7: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.8: Filtering peaks
Threshold=0.65: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.9: Filtering peaks
Threshold=0.75: Filtering peaks
Computing precision-recall results.
Computing precision-recall results.
Threshold=0.85: Filtering peaks
Computing precision-recall results.
Threshold=0.95: Filtering peaks
Computing precision-recall results.
Reformatting precision-recall data.
Saving precision-recall results ==> /tmp/RtmpWxJYrw/file26c43d4efceff1precision_recall.csv
Plotting precision-recall curve.
Plotting F1.
Making predictions for peaklist1: CnR_H3K27ac
Making predictions for peaklist2: encode_H3K27ac
+ Predicting recall from 10 precision values.
+ Predicting precision from 10 recall values.
Making predictions for peaklist1: CnT_H3K27ac
Making predictions for peaklist2: encode_H3K27ac
+ Predicting recall from 10 precision values.
+ Predicting precision from 10 recall values.
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
--- Running tss_plot() ---
>> Running bootstrapping for tag matrix...		 2024-04-15 22:41:29 
>> Running bootstrapping for tag matrix...		 2024-04-15 22:41:29 
Done.
--- Running width_boxplot() ---
Done.
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 92 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
243.870  40.283 281.026