Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:09 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 649/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
EpiCompare 1.7.3 (landing page) Thomas Roberts
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.7.3 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EpiCompare_1.7.3.tar.gz |
StartedAt: 2024-03-02 03:36:30 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 04:01:04 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 1474.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: EpiCompare.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EpiCompare_1.7.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/EpiCompare.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘EpiCompare/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EpiCompare’ version ‘1.7.3’ * 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 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 77.501 4.977 102.283 predict_precision_recall 32.272 13.378 16.433 plot_ChIPseeker_annotation 40.782 2.491 70.471 plot_precision_recall 17.119 4.690 27.455 EpiCompare 17.573 1.776 37.923 plot_corr 12.764 3.012 14.298 rebin_peaks 8.204 3.514 9.665 compute_corr 7.143 2.916 8.461 liftover_grlist 6.809 1.599 23.190 plot_chromHMM 6.174 0.977 7.347 tss_plot 4.212 0.520 6.059 overlap_heatmap 4.110 0.354 9.533 precision_recall 0.130 0.079 34.685 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 33. ├─patchwork (local) FUN(X[[i]], ...) 34. └─patchwork:::plot_table.ggplot(X[[i]], ...) 35. └─ggplot2::ggplotGrob(x) 36. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 37. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 38. └─ggplot2:::plot_theme(plot) 39. └─ggplot2:::validate_theme(theme) 40. └─base::mapply(...) 41. └─ggplot2 (local) `<fn>`(...) 42. └─cli::cli_abort(...) 43. └─rlang::abort(...) [ FAIL 1 | WARN 7 | SKIP 0 | PASS 78 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/Users/biocbuild/bbs-3.19-bioc/meat/EpiCompare.Rcheck/00check.log’ for details.
EpiCompare.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EpiCompare ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)
EpiCompare.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 Quitting from lines 345-359 [overlap_upset_plot] (EpiCompare.Rmd) [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 0.01 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 1.09 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 7 seconds. Saving correlation results ==> /tmp/RtmpfOmZjw/file1708757567c32.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 7 seconds. Saving correlation results ==> /tmp/RtmpfOmZjw/file170876ef3e369.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 10 seconds. Saving correlation results ==> /tmp/RtmpfOmZjw/file170874dd73b67.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 14 seconds. Saving correlation results ==> /tmp/RtmpfOmZjw/file170876d7d0f1d.corr.csv.gz --- Running fragment_info() --- Done. Writing ==> /tmp/RtmpfOmZjw/processed_results/encode_H3K27ac.narrowPeaks.bed Writing ==> /tmp/RtmpfOmZjw/processed_results/CnT_H3K27ac.narrowPeaks.bed Writing ==> /tmp/RtmpfOmZjw/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/RtmpfOmZjw/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/local/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /private/tmp/RtmpfOmZjw/t1/EpiCompare.html --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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/RtmpfOmZjw/rmarkdown-str1708748b30ab.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: /private/tmp/RtmpfOmZjw/t1/EpiCompare.html [1] "Done in 0.28 min." All outputs saved to: /tmp/RtmpfOmZjw/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/local/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /private/tmp/RtmpfOmZjw/t2/EpiCompare.html --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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/RtmpfOmZjw/rmarkdown-str17087406fab13.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: /private/tmp/RtmpfOmZjw/t2/EpiCompare.html [1] "Done in 0.27 min." All outputs saved to: /tmp/RtmpfOmZjw/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/local/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /private/tmp/RtmpfOmZjw/t3/testthat_example_Mar_02_2024.html --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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/RtmpfOmZjw/rmarkdown-str1708732437a4c.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: /private/tmp/RtmpfOmZjw/t3/testthat_example_Mar_02_2024.html [1] "Done in 0.25 min." All outputs saved to: /tmp/RtmpfOmZjw/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 4.8s. --- Running overlap_heatmap() --- Genreating precision-recall matrix. overlap_heatmap(): Done in 0.3s. --- 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 13 seconds. Saving correlation results ==> /tmp/RtmpfOmZjw/file17087413e3e2e.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=0.55: Filtering peaks Threshold=0.5: 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/RtmpfOmZjw/file170876f044f2aprecision_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... 2024-03-02 04:00:38 >> Running bootstrapping for tag matrix... 2024-03-02 04:00:38 Done. --- Running width_boxplot() --- Done. [ FAIL 1 | WARN 7 | SKIP 0 | PASS 78 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-EpiCompare.R:16:3'): EpiCompare works ────────────────────────── Error in `plot_theme(plot)`: The `legend.text.align` theme element is not defined in the element hierarchy. Backtrace: ▆ 1. ├─EpiCompare::EpiCompare(...) at test-EpiCompare.R:16:3 2. │ └─rmarkdown::render(...) 3. │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 4. │ └─knitr:::process_file(text, output) 5. │ ├─knitr:::handle_error(...) 6. │ │ └─base::withCallingHandlers(...) 7. │ ├─base::withCallingHandlers(...) 8. │ ├─knitr:::process_group(group) 9. │ └─knitr:::process_group.block(group) 10. │ └─knitr:::call_block(x) 11. │ └─knitr:::block_exec(params) 12. │ └─knitr:::eng_r(options) 13. │ ├─knitr:::in_input_dir(...) 14. │ │ └─knitr:::in_dir(input_dir(), expr) 15. │ └─knitr (local) evaluate(...) 16. │ └─evaluate::evaluate(...) 17. │ └─evaluate:::evaluate_call(...) 18. │ ├─base (local) handle(...) 19. │ ├─base::withCallingHandlers(...) 20. │ ├─base::withVisible(value_fun(ev$value, ev$visible)) 21. │ └─knitr (local) value_fun(ev$value, ev$visible) 22. │ └─knitr (local) fun(x, options = options) 23. │ ├─base::withVisible(knit_print(x, ...)) 24. │ ├─knitr::knit_print(x, ...) 25. │ └─knitr:::knit_print.default(x, ...) 26. │ └─evaluate (local) normal_print(x) 27. │ ├─base::print(x) 28. │ └─base::print.default(x) 29. ├─base (local) `<fn>`(x) 30. └─patchwork:::print.patchwork(x) 31. └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto") 32. └─base::lapply(x$plots, plot_table, guides = guides) 33. ├─patchwork (local) FUN(X[[i]], ...) 34. └─patchwork:::plot_table.ggplot(X[[i]], ...) 35. └─ggplot2::ggplotGrob(x) 36. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 37. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 38. └─ggplot2:::plot_theme(plot) 39. └─ggplot2:::validate_theme(theme) 40. └─base::mapply(...) 41. └─ggplot2 (local) `<fn>`(...) 42. └─cli::cli_abort(...) 43. └─rlang::abort(...) [ FAIL 1 | WARN 7 | SKIP 0 | PASS 78 ] Error: Test failures Execution halted
EpiCompare.Rcheck/EpiCompare-Ex.timings
name | user | system | elapsed | |
EpiCompare | 17.573 | 1.776 | 37.923 | |
bpplapply | 0.013 | 0.037 | 0.059 | |
check_workers | 0.004 | 0.012 | 0.020 | |
compute_consensus_peaks | 1.142 | 0.292 | 1.755 | |
compute_corr | 7.143 | 2.916 | 8.461 | |
download_button | 0.007 | 0.004 | 0.026 | |
fragment_info | 0.006 | 0.008 | 0.025 | |
gather_files | 1.061 | 0.377 | 2.440 | |
group_files | 0.520 | 0.390 | 0.242 | |
liftover_grlist | 6.809 | 1.599 | 23.190 | |
overlap_heatmap | 4.110 | 0.354 | 9.533 | |
overlap_percent | 0.614 | 0.046 | 1.367 | |
overlap_stat_plot | 0.279 | 0.021 | 0.637 | |
overlap_upset_plot | 0.784 | 0.054 | 2.046 | |
peak_info | 1.749 | 0.153 | 4.562 | |
plot_ChIPseeker_annotation | 40.782 | 2.491 | 70.471 | |
plot_chromHMM | 6.174 | 0.977 | 7.347 | |
plot_corr | 12.764 | 3.012 | 14.298 | |
plot_enrichment | 77.501 | 4.977 | 102.283 | |
plot_precision_recall | 17.119 | 4.690 | 27.455 | |
precision_recall | 0.130 | 0.079 | 34.685 | |
predict_precision_recall | 32.272 | 13.378 | 16.433 | |
rebin_peaks | 8.204 | 3.514 | 9.665 | |
report_command | 0.001 | 0.000 | 0.000 | |
report_header | 0.002 | 0.002 | 0.007 | |
tidy_peakfile | 1.003 | 0.264 | 1.591 | |
translate_genome | 0.021 | 0.006 | 0.033 | |
tss_plot | 4.212 | 0.520 | 6.059 | |
width_boxplot | 0.102 | 0.013 | 0.137 | |
write_example_peaks | 0.398 | 0.028 | 0.522 | |