Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 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 328/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
chipenrich 2.29.0 (landing page) Kai Wang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the chipenrich package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chipenrich.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: chipenrich |
Version: 2.29.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chipenrich.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings chipenrich_2.29.0.tar.gz |
StartedAt: 2024-06-10 00:51:47 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 01:01:21 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 574.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: chipenrich.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chipenrich.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings chipenrich_2.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/chipenrich.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'chipenrich/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'chipenrich' version '2.29.0' * 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 whether package 'chipenrich' 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 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) broadenrich.Rd:134: Escaped LaTeX specials: \& checkRd: (-1) chipenrich.Rd:148: Escaped LaTeX specials: \& checkRd: (-1) hybridenrich.Rd:111: Escaped LaTeX specials: \& checkRd: (-1) polyenrich.Rd:148: Escaped LaTeX specials: \& checkRd: (-1) proxReg.Rd:117: Escaped LaTeX specials: \& * 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 files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed broadenrich 8.05 0.42 8.50 polyenrich 7.38 0.30 7.68 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'F:/biocbuild/bbs-3.20-bioc/meat/chipenrich.Rcheck/00check.log' for details.
chipenrich.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL chipenrich ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'chipenrich' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (chipenrich)
chipenrich.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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(chipenrich) > > test_check("chipenrich") [ FAIL 0 | WARN 0 | SKIP 3 | PASS 170 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • empty test (3): 'test_5_chipenrich.R:199:1', 'test_5_chipenrich.R:232:1', 'test_5_chipenrich.R:236:1' [ FAIL 0 | WARN 0 | SKIP 3 | PASS 170 ] > > proc.time() user system elapsed 194.00 18.73 213.23
chipenrich.Rcheck/chipenrich-Ex.timings
name | user | system | elapsed | |
assign_peak_segments | 0.36 | 0.02 | 0.52 | |
assign_peaks | 0.78 | 0.00 | 0.78 | |
broadenrich | 8.05 | 0.42 | 8.50 | |
calc_peak_gene_overlap | 0.47 | 0.02 | 0.49 | |
chipenrich | 2.34 | 0.12 | 2.48 | |
load_peaks | 0.06 | 0.00 | 0.07 | |
num_peaks_per_gene | 0.43 | 0.00 | 0.44 | |
peaks2genes | 0.60 | 0.02 | 0.62 | |
plot_chipenrich_spline | 1.30 | 0.17 | 1.47 | |
plot_dist_to_tss | 0.29 | 0.00 | 0.30 | |
plot_gene_coverage | 0.86 | 0.01 | 0.87 | |
plot_polyenrich_spline | 2.06 | 0.23 | 2.30 | |
polyenrich | 7.38 | 0.30 | 7.68 | |
proxReg | 0.48 | 0.03 | 0.52 | |
read_bed | 0.22 | 0.03 | 0.31 | |
supported_genesets | 0.02 | 0.00 | 0.02 | |
supported_genomes | 0 | 0 | 0 | |
supported_locusdefs | 0.01 | 0.00 | 0.01 | |
supported_methods | 0 | 0 | 0 | |
supported_read_lengths | 0.02 | 0.00 | 0.02 | |