Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-03 11:47 -0400 (Thu, 03 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4716 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
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 952/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HiContacts 1.7.1 (landing page) Jacques Serizay
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the HiContacts package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiContacts.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: HiContacts |
Version: 1.7.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiContacts.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiContacts_1.7.1.tar.gz |
StartedAt: 2024-10-02 21:51:29 -0400 (Wed, 02 Oct 2024) |
EndedAt: 2024-10-02 21:54:49 -0400 (Wed, 02 Oct 2024) |
EllapsedTime: 200.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: HiContacts.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiContacts.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiContacts_1.7.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/HiContacts.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘HiContacts/DESCRIPTION’ ... OK * this is package ‘HiContacts’ version ‘1.7.1’ * 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 ‘HiContacts’ 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed arithmetics 18.612 2.475 21.430 Contacts 7.359 0.493 8.357 tracks 5.633 0.899 6.896 getCompartments 4.367 1.510 4.431 plotMatrix 4.515 0.499 5.189 * 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: OK
HiContacts.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HiContacts ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘HiContacts’ ... ** 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 (HiContacts)
HiContacts.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(HiContacts) Loading required package: HiCExperiment Consider using the `HiContacts` package to perform advanced genomic operations on `HiCExperiment` objects. Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more: https://js2264.github.io/OHCA/ > > test_check("HiContacts") [ FAIL 0 | WARN 1 | SKIP 0 | PASS 51 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 51 ] > > proc.time() user system elapsed 53.122 8.122 63.043
HiContacts.Rcheck/HiContacts-Ex.timings
name | user | system | elapsed | |
Contacts | 7.359 | 0.493 | 8.357 | |
Ps | 1.353 | 0.144 | 1.679 | |
arithmetics | 18.612 | 2.475 | 21.430 | |
cisTransRatio | 1.139 | 0.248 | 1.593 | |
getCompartments | 4.367 | 1.510 | 4.431 | |
getDiamondInsulation | 1.558 | 0.741 | 2.077 | |
palettes | 0 | 0 | 0 | |
plot4C | 1.058 | 0.265 | 1.511 | |
plotMatrix | 4.515 | 0.499 | 5.189 | |
plotPs | 3.017 | 0.410 | 3.903 | |
plotScalogram | 2.434 | 0.334 | 3.083 | |
scalogram | 2.376 | 0.266 | 2.855 | |
tracks | 5.633 | 0.899 | 6.896 | |
virtual4C | 0.931 | 0.152 | 1.288 | |