Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 323/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Chicago 1.35.0 (landing page) Mikhail Spivakov
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the Chicago package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Chicago.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: Chicago |
Version: 1.35.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Chicago.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Chicago_1.35.0.tar.gz |
StartedAt: 2024-12-23 18:34:24 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 18:35:06 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 41.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Chicago.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Chicago.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Chicago_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Chicago.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Chicago/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Chicago’ version ‘1.35.0’ * 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 ‘Chicago’ 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 whether startup messages can be suppressed ... 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: overlapFragWithFeatures.Rd: data.table peakEnrichment4Features.Rd: data.table Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 exportResults 6.306 0.244 6.561 normaliseOtherEnds 5.949 0.547 6.539 * 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/Chicago.Rcheck/00check.log’ for details.
Chicago.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Chicago ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘Chicago’ ... ** using staged installation ** R ** data ** 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 (Chicago)
Chicago.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 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. > library(testthat) > library(Chicago) Loading required package: data.table Welcome to CHiCAGO - version 1.35.0 If you are new to CHiCAGO, please consider reading the vignette through the command: vignette("Chicago"). NOTE: Default values of tlb.minProxOEPerBin and tlb.minProxB2BPerBin changed as of Version 1.1.5. No action is required unless you specified non-default values, or wish to re-run the pipeline on old chicagoData objects. See news(package="Chicago") > > test_check("Chicago") Read 4 items Read 4 items Read 4 items [ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ] > > proc.time() user system elapsed 0.812 0.079 0.891
Chicago.Rcheck/Chicago-Ex.timings
name | user | system | elapsed | |
cdUnitTest | 0.022 | 0.003 | 0.027 | |
chicagoData | 0.001 | 0.000 | 0.000 | |
chicagoPipeline | 0.013 | 0.002 | 0.015 | |
copyCD | 0.002 | 0.001 | 0.003 | |
defaultSettings | 0.001 | 0.000 | 0.000 | |
estimateBrownianComponent | 0.055 | 0.004 | 0.060 | |
estimateDistFun | 0.008 | 0.002 | 0.010 | |
estimateTechnicalNoise | 0.022 | 0.002 | 0.024 | |
exportResults | 6.306 | 0.244 | 6.561 | |
getPvals | 0.015 | 0.001 | 0.015 | |
getScores | 0.013 | 0.001 | 0.015 | |
getSkOnly | 0.024 | 0.002 | 0.027 | |
mergeSamples | 0.029 | 0.003 | 0.031 | |
modifySettings | 0.012 | 0.001 | 0.013 | |
normaliseBaits | 0.025 | 0.003 | 0.028 | |
normaliseOtherEnds | 5.949 | 0.547 | 6.539 | |
overlapFragWithFeatures | 0.020 | 0.002 | 0.022 | |
peakEnrichment4Features | 0.270 | 0.024 | 0.293 | |
plotBaits | 0.038 | 0.005 | 0.043 | |
plotDistFun | 0.030 | 0.002 | 0.030 | |
readAndMerge | 0.023 | 0.003 | 0.027 | |
readSample | 0.011 | 0.002 | 0.014 | |
setExperiment | 0.008 | 0.001 | 0.009 | |