Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:40 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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 |
To the developers/maintainers of the EpiCompare package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 609/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
EpiCompare 1.3.4 (landing page) Sera Choi
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: EpiCompare |
Version: 1.3.4 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings EpiCompare_1.3.4.tar.gz |
StartedAt: 2023-02-28 02:40:37 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 02:57:04 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 987.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: EpiCompare.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings EpiCompare_1.3.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/EpiCompare.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘EpiCompare/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EpiCompare’ version ‘1.3.4’ * 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 55.216 2.417 60.012 plot_ChIPseeker_annotation 31.405 1.264 32.670 predict_precision_recall 12.951 1.825 5.211 plot_corr 10.195 2.210 10.203 rebin_peaks 9.722 2.677 4.980 plot_precision_recall 10.041 1.568 6.627 EpiCompare 9.949 0.835 10.844 liftover_grlist 5.925 1.489 11.355 compute_corr 3.655 1.815 3.316 plot_chromHMM 4.696 0.531 6.309 * 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: ▆ 1. └─EpiCompare::liftover_grlist(...) at test-liftover_grlist.R:24:4 2. └─EpiCompare:::get_chain_file(...) 3. ├─ah[["AH14155"]] 4. └─ah[["AH14155"]] 5. └─AnnotationHub (local) .local(x, i, j = j, ...) 6. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 7. └─base::tryCatch(...) 8. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10. └─value[[3L]](cond) [ FAIL 1 | WARN 5 | SKIP 0 | PASS 95 ] Error: Test failures Execution halted * 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 ‘example_report.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.17-bioc/meat/EpiCompare.Rcheck/00check.log’ for details.
EpiCompare.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL EpiCompare ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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/RtmpriD2e1/EpiCompare_testthat/EpiCompare.html --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/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-3.17-bioc/R/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/RtmpriD2e1/rmarkdown-str50131469b256e.html --variable code_folding=hide --variable code_menu=1 [WARNING] This document format requires a nonempty <title> element. Defaulting to 'EpiCompare.knit' as the title. To specify a title, use 'title' in metadata or --metadata title="...". Output created: /tmp/RtmpriD2e1/EpiCompare_testthat/EpiCompare.html [1] "Done in 2.71 min." All outputs saved to: /tmp/RtmpriD2e1/EpiCompare_testthat 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/RtmpriD2e1/EpiCompare_testthat/EpiCompare.html --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/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-3.17-bioc/R/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/RtmpriD2e1/rmarkdown-str501317ec4903f.html --variable code_folding=hide --variable code_menu=1 [WARNING] This document format requires a nonempty <title> element. Defaulting to 'EpiCompare.knit' as the title. To specify a title, use 'title' in metadata or --metadata title="...". Output created: /tmp/RtmpriD2e1/EpiCompare_testthat/EpiCompare.html [1] "Done in 0.14 min." All outputs saved to: /tmp/RtmpriD2e1/EpiCompare_testthat [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 0.6 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 3 seconds. Saving correlation results ==> /tmp/RtmpriD2e1/file501311d44878.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/RtmpriD2e1/file501311b42065.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 6 seconds. Saving correlation results ==> /tmp/RtmpriD2e1/file501317a96c888.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 13 seconds. Saving correlation results ==> /tmp/RtmpriD2e1/file5013137f33f33.corr.csv.gz --- Running fragment_info() --- Done. Writing ==> /tmp/RtmpriD2e1/processed_results/encode_H3K27ac.narrowPeaks.bed Writing ==> /tmp/RtmpriD2e1/processed_results/CnT_H3K27ac.narrowPeaks.bed Writing ==> /tmp/RtmpriD2e1/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/RtmpriD2e1/processed_results/encode_H3K27ac.narrowPeaks.bed Preparing chain file. snapshotDate(): 2022-12-16 loading from cache require("rtracklayer") Performing liftover: hg19 --> hg38 Removing non-standard chromosomes. Preparing chain file. snapshotDate(): 2022-12-16 Preparing chain file. snapshotDate(): 2022-12-16 loading from cache Performing liftover: hg38 --> hg19 Removing non-standard chromosomes. loading from cache 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/RtmpriD2e1/EpiCompare_test/EpiCompare.html --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/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-3.17-bioc/R/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/RtmpriD2e1/rmarkdown-str501313962599f.html --variable code_folding=hide --variable code_menu=1 [WARNING] This document format requires a nonempty <title> element. Defaulting to 'EpiCompare.knit' as the title. To specify a title, use 'title' in metadata or --metadata title="...". Output created: /tmp/RtmpriD2e1/EpiCompare_test/EpiCompare.html [1] "Done in 0.11 min." All outputs saved to: /tmp/RtmpriD2e1/EpiCompare_test 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/RtmpriD2e1/EpiCompare_test/EpiCompare.html --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/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-3.17-bioc/R/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/RtmpriD2e1/rmarkdown-str5013134c8c393.html --variable code_folding=hide --variable code_menu=1 [WARNING] This document format requires a nonempty <title> element. Defaulting to 'EpiCompare.knit' as the title. To specify a title, use 'title' in metadata or --metadata title="...". Output created: /tmp/RtmpriD2e1/EpiCompare_test/EpiCompare.html [1] "Done in 0.12 min." All outputs saved to: /tmp/RtmpriD2e1/EpiCompare_test 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/RtmpriD2e1/EpiCompare_test/testthat_example_Feb_28_2023.html --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/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-3.17-bioc/R/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/RtmpriD2e1/rmarkdown-str5013111d21d30.html --variable code_folding=hide --variable code_menu=1 [WARNING] This document format requires a nonempty <title> element. Defaulting to 'EpiCompare.knit' as the title. To specify a title, use 'title' in metadata or --metadata title="...". Output created: /tmp/RtmpriD2e1/EpiCompare_test/testthat_example_Feb_28_2023.html [1] "Done in 0.11 min." All outputs saved to: /tmp/RtmpriD2e1/EpiCompare_test --- 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 0.7s. --- 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 9 seconds. Saving correlation results ==> /tmp/RtmpriD2e1/file50131794cd601.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. Threshold=0.3: Filtering peaks Computing precision-recall results. Threshold=0.35: Filtering peaks Computing precision-recall results. Threshold=0.4: Filtering peaks Computing precision-recall results. Threshold=0.5: Filtering peaks Computing precision-recall results. Threshold=0.6: Filtering peaks Computing precision-recall results. Threshold=0.45: Filtering peaks Computing precision-recall results. Threshold=0.7: Filtering peaks Computing precision-recall results. Threshold=0.55: 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=0.75: Filtering peaks Threshold=0.9: 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/RtmpriD2e1/file50131114f75bcprecision_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... 2023-02-28 02:54:54 >> Running bootstrapping for tag matrix... 2023-02-28 02:54:56 Done. --- Running width_boxplot() --- Done. [ FAIL 1 | WARN 5 | SKIP 0 | PASS 95 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-liftover_grlist.R:24'): liftover_grlist works ────────────────── Error: failed to load resource name: AH14155 title: hg19ToMm9.over.chain.gz reason: incomplete block Backtrace: ▆ 1. └─EpiCompare::liftover_grlist(...) at test-liftover_grlist.R:24:4 2. └─EpiCompare:::get_chain_file(...) 3. ├─ah[["AH14155"]] 4. └─ah[["AH14155"]] 5. └─AnnotationHub (local) .local(x, i, j = j, ...) 6. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 7. └─base::tryCatch(...) 8. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10. └─value[[3L]](cond) [ FAIL 1 | WARN 5 | SKIP 0 | PASS 95 ] Error: Test failures Execution halted
EpiCompare.Rcheck/EpiCompare-Ex.timings
name | user | system | elapsed | |
EpiCompare | 9.949 | 0.835 | 10.844 | |
bpplapply | 0.010 | 0.058 | 0.066 | |
check_workers | 0.004 | 0.001 | 0.004 | |
compute_consensus_peaks | 0.735 | 0.261 | 0.903 | |
compute_corr | 3.655 | 1.815 | 3.316 | |
download_button | 0.000 | 0.007 | 0.007 | |
fragment_info | 0.004 | 0.001 | 0.005 | |
gather_files | 0.665 | 0.248 | 0.952 | |
group_files | 0.300 | 0.153 | 0.071 | |
liftover_grlist | 5.925 | 1.489 | 11.355 | |
overlap_heatmap | 0.816 | 0.080 | 0.896 | |
overlap_percent | 0.418 | 0.044 | 0.462 | |
overlap_stat_plot | 0.238 | 0.015 | 0.253 | |
overlap_upset_plot | 0.461 | 0.032 | 0.499 | |
peak_info | 1.024 | 0.092 | 1.116 | |
plot_ChIPseeker_annotation | 31.405 | 1.264 | 32.670 | |
plot_chromHMM | 4.696 | 0.531 | 6.309 | |
plot_corr | 10.195 | 2.210 | 10.203 | |
plot_enrichment | 55.216 | 2.417 | 60.012 | |
plot_precision_recall | 10.041 | 1.568 | 6.627 | |
precision_recall | 0.081 | 0.096 | 4.879 | |
predict_precision_recall | 12.951 | 1.825 | 5.211 | |
rebin_peaks | 9.722 | 2.677 | 4.980 | |
report_command | 0 | 0 | 0 | |
report_header | 0.002 | 0.000 | 0.001 | |
tidy_peakfile | 0.524 | 0.120 | 0.644 | |
translate_genome | 0.012 | 0.004 | 0.016 | |
tss_plot | 4.213 | 0.548 | 4.761 | |
width_boxplot | 0.066 | 0.001 | 0.066 | |
write_example_peaks | 0.233 | 0.015 | 0.248 | |