Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
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" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1432/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
nucleR 2.38.0 (landing page) Alba Sala
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the nucleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/nucleR.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: nucleR |
Version: 2.38.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nucleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nucleR_2.38.0.tar.gz |
StartedAt: 2024-12-20 07:02:06 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 07:11:55 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 589.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: nucleR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nucleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nucleR_2.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/nucleR.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘nucleR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘nucleR’ version ‘2.38.0’ * 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 ‘nucleR’ 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 ... NOTE Unknown package ‘Starr’ in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'dot-fftRegion.Rd' ‘data2’ ‘pcKeepComp’ Undocumented arguments in Rd file 'dot-loadFiles.Rd' ‘singleLoad’ ‘pairedLoad’ Undocumented arguments in Rd file 'dot-loadPairedBam.Rd' ‘file’ Undocumented arguments in Rd file 'dot-loadSingleBam.Rd' ‘exp’ Undocumented arguments in Rd file 'dot-mid.Rd' ‘x’ Undocumented arguments in Rd file 'dot-unlist_as_integer.Rd' ‘x’ Undocumented arguments in Rd file 'dot-xlapply.Rd' ‘X’ ‘FUN’ ‘...’ ‘mc.cores’ Documented arguments not in \usage in Rd file 'pcKeepCompDetect.Rd': ‘...’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 syntheticNucMap 95.578 0.908 97.737 * 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 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/nucleR.Rcheck/00check.log’ for details.
nucleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL nucleR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘nucleR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Loading required package: usethis Welcome at Thu Dec 19 15:49:22 2024 Goodbye at Thu Dec 19 15:49:45 2024 ** help *** installing help indices ** building package indices Loading required package: usethis Welcome at Thu Dec 19 15:49:48 2024 Goodbye at Thu Dec 19 15:49:48 2024 ** installing vignettes ** testing if installed package can be loaded from temporary location Loading required package: usethis Welcome at Thu Dec 19 15:49:51 2024 Goodbye at Thu Dec 19 15:50:11 2024 ** testing if installed package can be loaded from final location Loading required package: usethis Welcome at Thu Dec 19 15:50:14 2024 Goodbye at Thu Dec 19 15:50:33 2024 ** testing if installed package keeps a record of temporary installation path * DONE (nucleR)
nucleR.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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(nucleR) > > test_check("nucleR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ] > > proc.time() user system elapsed 20.619 1.077 22.110
nucleR.Rcheck/nucleR-Ex.timings
name | user | system | elapsed | |
controlCorrection | 0.173 | 0.023 | 0.197 | |
coverage.rpm | 0.777 | 0.067 | 0.886 | |
export.bed | 0.308 | 0.020 | 0.330 | |
export.wig | 0.135 | 0.246 | 0.382 | |
filterFFT | 1.127 | 0.028 | 1.207 | |
fragmentLenDetect | 1.124 | 0.067 | 1.204 | |
mergeCalls | 1.270 | 0.011 | 1.294 | |
nucleR-package | 4.296 | 0.050 | 4.473 | |
pcKeepCompDetect | 0.675 | 0.034 | 0.718 | |
peakDetection | 3.830 | 0.159 | 4.115 | |
peakScoring | 0.892 | 0.017 | 0.912 | |
plotPeaks | 2.898 | 0.027 | 2.936 | |
processReads | 0.712 | 0.049 | 0.777 | |
processTilingArray | 0.001 | 0.001 | 0.002 | |
readBAM | 0.234 | 0.007 | 0.253 | |
syntheticNucMap | 95.578 | 0.908 | 97.737 | |