Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:07 -0400 (Thu, 18 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
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 331/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
chipenrich 2.26.0 (landing page) Kai Wang
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | |||||||
To the developers/maintainers of the chipenrich package: - 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: 2.26.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chipenrich.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chipenrich_2.26.0.tar.gz |
StartedAt: 2024-04-17 08:43:41 -0400 (Wed, 17 Apr 2024) |
EndedAt: 2024-04-17 08:53:20 -0400 (Wed, 17 Apr 2024) |
EllapsedTime: 579.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: chipenrich.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chipenrich.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chipenrich_2.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/chipenrich.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘chipenrich/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘chipenrich’ version ‘2.26.0’ * 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 for sufficient/correct file permissions ... 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 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 ... 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 9.382 0.529 10.007 polyenrich 6.683 0.343 7.095 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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 ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/chipenrich.Rcheck/00check.log’ for details.
chipenrich.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL chipenrich ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 (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(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 199.430 14.604 216.495
chipenrich.Rcheck/chipenrich-Ex.timings
name | user | system | elapsed | |
assign_peak_segments | 0.369 | 0.017 | 0.389 | |
assign_peaks | 0.688 | 0.014 | 0.703 | |
broadenrich | 9.382 | 0.529 | 10.007 | |
calc_peak_gene_overlap | 0.392 | 0.021 | 0.415 | |
chipenrich | 1.729 | 0.097 | 1.854 | |
load_peaks | 0.058 | 0.001 | 0.063 | |
num_peaks_per_gene | 0.564 | 0.022 | 0.594 | |
peaks2genes | 0.560 | 0.021 | 0.586 | |
plot_chipenrich_spline | 1.673 | 0.211 | 1.902 | |
plot_dist_to_tss | 0.436 | 0.014 | 0.453 | |
plot_gene_coverage | 0.951 | 0.043 | 1.001 | |
plot_polyenrich_spline | 3.210 | 0.219 | 3.457 | |
polyenrich | 6.683 | 0.343 | 7.095 | |
proxReg | 0.555 | 0.016 | 0.576 | |
read_bed | 0.231 | 0.006 | 0.241 | |
supported_genesets | 0.007 | 0.001 | 0.008 | |
supported_genomes | 0.002 | 0.001 | 0.003 | |
supported_locusdefs | 0.006 | 0.003 | 0.009 | |
supported_methods | 0.001 | 0.001 | 0.001 | |
supported_read_lengths | 0.005 | 0.002 | 0.008 | |