Hiranyamaya Dash
| Snapshot Date: 2025-01-20 13:00 -0500 (Mon, 20 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/EpiCompare |
| git_branch: RELEASE_3_20 |
| git_last_commit: debc9b1 |
| git_last_commit_date: 2024-10-29 11:11:35 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-23 12:12 -0500 (Thu, 23 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4493 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4394 |
| 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 653/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EpiCompare 1.10.0 (landing page) Hiranyamaya Dash
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | 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 | | ||||||||
| taishan | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: EpiCompare |
| Version: 1.10.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings EpiCompare_1.10.0.tar.gz |
| StartedAt: 2025-01-21 06:44:18 -0000 (Tue, 21 Jan 2025) |
| EndedAt: 2025-01-21 07:24:18 -0000 (Tue, 21 Jan 2025) |
| EllapsedTime: 2400.1 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: EpiCompare.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings EpiCompare_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/EpiCompare.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EpiCompare/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EpiCompare’ version ‘1.10.0’
* 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:74-75: 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:82-84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:85-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:179: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:180: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiCompare.Rd:181: 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:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:40-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prepare_genome_builds.Rd:43-44: 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 ...
EpiCompare.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL EpiCompare ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.2/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)
EpiCompare.Rcheck/EpiCompare-Ex.timings
| name | user | system | elapsed | |
| EpiCompare | 12.685 | 1.050 | 20.568 | |
| bpplapply | 0.006 | 0.063 | 0.071 | |
| check_workers | 0.005 | 0.002 | 0.007 | |
| compute_consensus_peaks | 0.709 | 0.245 | 0.879 | |
| compute_corr | 4.038 | 1.327 | 4.231 | |
| download_button | 0.005 | 0.004 | 0.026 | |
| fragment_info | 0.005 | 0.000 | 0.005 | |
| gather_files | 0.515 | 0.262 | 0.874 | |
| group_files | 0.324 | 0.155 | 0.084 | |
| liftover_grlist | 4.393 | 0.755 | 8.861 | |
| overlap_heatmap | 3.156 | 0.459 | 3.626 | |
| overlap_percent | 0.439 | 0.012 | 0.453 | |
| overlap_stat_plot | 0.237 | 0.004 | 0.241 | |
| overlap_upset_plot | 0.488 | 0.008 | 0.504 | |
| peak_info | 1.073 | 0.076 | 1.153 | |
| plot_ChIPseeker_annotation | 27.314 | 0.510 | 28.222 | |
| plot_chromHMM | 5.203 | 0.592 | 15.056 | |
| plot_corr | 9.559 | 1.756 | 9.015 | |
| plot_enrichment | 48.077 | 1.989 | 52.915 | |
| plot_precision_recall | 10.181 | 2.486 | 7.121 | |
| precision_recall | 0.079 | 0.107 | 5.687 | |