Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-04 11:40 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 |
Package 667/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
EpiCompare 1.12.0 (landing page) Hiranyamaya Dash
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | TIMEOUT | ||||||||||
To the developers/maintainers of the EpiCompare package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EpiCompare.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: EpiCompare |
Version: 1.12.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings EpiCompare_1.12.0.tar.gz |
StartedAt: 2025-08-03 22:10:43 -0400 (Sun, 03 Aug 2025) |
EndedAt: 2025-08-03 22:24:02 -0400 (Sun, 03 Aug 2025) |
EllapsedTime: 799.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: EpiCompare.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings EpiCompare_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/EpiCompare.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘EpiCompare/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EpiCompare’ version ‘1.12.0’ * 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 code 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 ... NOTE checkRd: (-1) EpiCompare.Rd:51-53: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:54: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:55: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:76-77: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:78-79: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:80-81: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:82-83: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:84-86: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:87-88: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:181: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:182: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:183: Lost braces in \itemize; meant \describe ? checkRd: (-1) compute_consensus_peaks.Rd:45-47: Lost braces in \itemize; meant \describe ? checkRd: (-1) compute_consensus_peaks.Rd:48-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) compute_corr.Rd:62-65: Lost braces in \itemize; meant \describe ? checkRd: (-1) compute_corr.Rd:66-69: Lost braces in \itemize; meant \describe ? checkRd: (-1) compute_corr.Rd:70-72: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files.Rd:22-23: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files.Rd:26-27: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files.Rd:28-29: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files.Rd:60: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files.Rd:61-62: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files.Rd:63-65: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files_names.Rd:14-15: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files_names.Rd:16: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files_names.Rd:17: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files_names.Rd:18-19: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files_names.Rd:20-21: Lost braces in \itemize; meant \describe ? checkRd: (-1) liftover_grlist.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) liftover_grlist.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) overlap_stat_plot.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) overlap_stat_plot.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plot_corr.Rd:64-67: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_corr.Rd:68-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_corr.Rd:72-74: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_precision_recall.Rd:47-50: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_precision_recall.Rd:51-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_precision_recall.Rd:55-57: Lost braces in \itemize; meant \describe ? checkRd: (-1) precision_recall.Rd:42-45: Lost braces in \itemize; meant \describe ? checkRd: (-1) precision_recall.Rd:46-49: Lost braces in \itemize; meant \describe ? checkRd: (-1) precision_recall.Rd:50-52: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:13-15: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:16: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:17: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:33-34: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:35-36: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:37-38: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:39-40: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:41-43: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:44-45: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_peaks.Rd:14-15: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_peaks.Rd:16: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_peaks.Rd:17: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_peaks.Rd:18-19: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_peaks.Rd:20-21: Lost braces in \itemize; meant \describe ? checkRd: (-1) rebin_peaks.Rd:39-42: Lost braces in \itemize; meant \describe ? checkRd: (-1) rebin_peaks.Rd:43-46: Lost braces in \itemize; meant \describe ? checkRd: (-1) rebin_peaks.Rd:47-49: Lost braces in \itemize; meant \describe ? * 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 57.585 5.131 71.066 plot_ChIPseeker_annotation 23.443 2.117 25.607 EpiCompare 14.172 1.253 16.526 plot_corr 9.690 4.629 9.893 predict_precision_recall 9.168 1.964 4.201 rebin_peaks 7.652 2.090 3.875 plot_precision_recall 6.795 1.503 4.603 gather_files 5.370 2.094 1.516 liftover_grlist 5.539 1.314 7.603 compute_corr 2.404 1.211 8.433 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/EpiCompare.Rcheck/00check.log’ for details.
EpiCompare.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL EpiCompare ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘EpiCompare’ ... ** this is package ‘EpiCompare’ version ‘1.12.0’ ** 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)
EpiCompare.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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/RtmpDhAAve/t1/EpiCompare.html --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.21-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-3.21-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/RtmpDhAAve/rmarkdown-str2cf2f2464efc8f.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/RtmpDhAAve/t1/EpiCompare.html [1] "Done in 2.34 min." All outputs saved to: /tmp/RtmpDhAAve/t1 [1] 1 [1] 3 [1] 5 [1] 7 [1] 9 [1] 11 [1] 13 [1] 15 [1] 17 [1] 19 [1] 21 [1] 23 [1] 25 [1] 2 [1] 4 [1] 6 [1] 8 [1] 10 [1] 12 [1] 14 [1] 16 [1] 18 [1] 20 [1] 22 [1] 24 [1] 26 [1] 1 [1] 2 [1] 3 [1] 4 [1] 5 [1] 6 [1] 7 [1] 8 [1] 9 [1] 10 [1] 11 [1] 12 [1] 13 [1] 14 [1] 15 [1] 16 [1] 17 [1] 18 [1] 19 [1] 20 [1] 21 [1] 22 [1] 23 [1] 24 [1] 25 [1] 26 [1] 1 [1] 2 [1] 3 [1] 4 [1] 5 [1] 6 [1] 7 [1] 8 [1] 9 [1] 10 [1] 11 [1] 12 [1] 13 [1] 14 [1] 15 [1] 16 [1] 17 [1] 18 [1] 19 [1] 20 [1] 21 [1] 22 [1] 23 [1] 24 [1] 25 [1] 26 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 0.4 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/RtmpDhAAve/file2cf2f2b878292.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/RtmpDhAAve/file2cf2f22daa514c.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/RtmpDhAAve/file2cf2f223fee4f1.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 8 seconds. Saving correlation results ==> /tmp/RtmpDhAAve/file2cf2f245c53b09.corr.csv.gz --- Running fragment_info() --- Done. Writing ==> /tmp/RtmpDhAAve/processed_results/encode_H3K27ac.narrowPeaks.bed Writing ==> /tmp/RtmpDhAAve/processed_results/CnT_H3K27ac.narrowPeaks.bed Writing ==> /tmp/RtmpDhAAve/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/RtmpDhAAve/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/RtmpDhAAve/t1/EpiCompare.html --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.21-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-3.21-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/RtmpDhAAve/rmarkdown-str2cf2f26bd17f76.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/RtmpDhAAve/t1/EpiCompare.html [1] "Done in 0.12 min." All outputs saved to: /tmp/RtmpDhAAve/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/RtmpDhAAve/t2/EpiCompare.html --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.21-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-3.21-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/RtmpDhAAve/rmarkdown-str2cf2f233bca90a.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/RtmpDhAAve/t2/EpiCompare.html [1] "Done in 0.13 min." All outputs saved to: /tmp/RtmpDhAAve/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/RtmpDhAAve/t3/testthat_example_Aug_03_2025.html --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.21-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-3.21-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/RtmpDhAAve/rmarkdown-str2cf2f27a30faa7.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/RtmpDhAAve/t3/testthat_example_Aug_03_2025.html [1] "Done in 0.12 min." All outputs saved to: /tmp/RtmpDhAAve/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 3s. --- 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/RtmpDhAAve/file2cf2f2238d9406.corr.csv.gz Threshold=0: Filtering peaks Threshold=0.05: Filtering peaks Computing precision-recall results. Computing precision-recall results. Threshold=0.1: Filtering peaks Threshold=0.15: Filtering peaks Computing precision-recall results. Computing precision-recall results. Threshold=0.2: Filtering peaks Threshold=0.25: Filtering peaks Computing precision-recall results. Computing precision-recall results. Threshold=0.3: Filtering peaks Threshold=0.35: Filtering peaks Computing precision-recall results. Computing precision-recall results. Threshold=0.4: Filtering peaks Threshold=0.45: Filtering peaks Computing precision-recall results. Computing precision-recall results. Threshold=0.5: Filtering peaks Threshold=0.55: Filtering peaks Computing precision-recall results. Computing precision-recall results. Threshold=0.6: Filtering peaks Threshold=0.65: Filtering peaks Computing precision-recall results. Computing precision-recall results. Threshold=0.7: Filtering peaks Threshold=0.75: Filtering peaks Computing precision-recall results. Computing precision-recall results. Threshold=0.8: Filtering peaks Threshold=0.85: Filtering peaks Computing precision-recall results. Computing precision-recall results. Threshold=0.9: Filtering peaks Threshold=0.95: Filtering peaks Computing precision-recall results. Computing precision-recall results. Reformatting precision-recall data. Saving precision-recall results ==> /tmp/RtmpDhAAve/file2cf2f2375dd579precision_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... 2025-08-03 22:23:13 >> Running bootstrapping for tag matrix... 2025-08-03 22:23:13 Done. --- Running width_boxplot() --- Done. [ FAIL 0 | WARN 7 | SKIP 0 | PASS 102 ] [ FAIL 0 | WARN 7 | SKIP 0 | PASS 102 ] > > proc.time() user system elapsed 252.958 36.309 281.170
EpiCompare.Rcheck/EpiCompare-Ex.timings
name | user | system | elapsed | |
EpiCompare | 14.172 | 1.253 | 16.526 | |
bpplapply | 0.007 | 0.189 | 0.286 | |
check_workers | 0.002 | 0.009 | 0.019 | |
compute_consensus_peaks | 0.909 | 0.389 | 1.367 | |
compute_corr | 2.404 | 1.211 | 8.433 | |
download_button | 0.005 | 0.003 | 0.016 | |
fragment_info | 0.005 | 0.000 | 0.007 | |
gather_files | 5.370 | 2.094 | 1.516 | |
group_files | 0.636 | 0.318 | 0.184 | |
liftover_grlist | 5.539 | 1.314 | 7.603 | |
overlap_heatmap | 3.417 | 0.713 | 4.134 | |
overlap_percent | 0.437 | 0.010 | 0.448 | |
overlap_stat_plot | 0.250 | 0.023 | 0.268 | |
overlap_upset_plot | 0.597 | 0.014 | 0.611 | |
peak_info | 1.040 | 0.124 | 1.164 | |
plot_ChIPseeker_annotation | 23.443 | 2.117 | 25.607 | |
plot_chromHMM | 2.948 | 0.408 | 3.850 | |
plot_corr | 9.690 | 4.629 | 9.893 | |
plot_enrichment | 57.585 | 5.131 | 71.066 | |
plot_precision_recall | 6.795 | 1.503 | 4.603 | |
precision_recall | 0.070 | 0.089 | 3.600 | |
predict_precision_recall | 9.168 | 1.964 | 4.201 | |
rebin_peaks | 7.652 | 2.090 | 3.875 | |
report_command | 0 | 0 | 0 | |
report_header | 0.001 | 0.000 | 0.002 | |
tidy_chromosomes | 1.009 | 0.084 | 1.094 | |
tidy_peakfile | 0.414 | 0.042 | 0.457 | |
translate_genome | 0.011 | 0.001 | 0.012 | |
tss_plot | 1.835 | 0.088 | 1.922 | |
width_boxplot | 0.056 | 0.002 | 0.058 | |
write_example_peaks | 0.178 | 0.000 | 0.178 | |