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 600/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Doscheda 1.28.0 (landing page) Bruno Contrino
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the Doscheda package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Doscheda.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: Doscheda |
Version: 1.28.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Doscheda.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Doscheda_1.28.0.tar.gz |
StartedAt: 2024-12-20 02:45:02 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 02:51:43 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 400.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Doscheda.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Doscheda.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Doscheda_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Doscheda.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 ‘Doscheda/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Doscheda’ version ‘1.28.0’ * 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 ‘Doscheda’ 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 ... NOTE Invalid package aliases in Rd file 'doscheda.Rd': ‘doscheda-package’ * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... 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 fitModel-methods 52.279 5.747 69.083 runDoscheda 45.629 0.272 54.142 pcaPlot-methods 9.092 0.127 14.551 runNormalisation-methods 4.862 2.202 9.772 corrPlot-methods 4.427 0.289 10.702 meanSdPlot-methods 4.125 0.080 6.694 volcanoPlot-methods 3.500 0.065 5.898 densityPlot-methods 3.468 0.070 6.383 replicatePlot-methods 3.452 0.081 5.988 * 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-3.20-bioc/meat/Doscheda.Rcheck/00check.log’ for details.
Doscheda.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Doscheda ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘Doscheda’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading in method for ‘getInput’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet” in method for ‘getNorm’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet” in method for ‘getFinal’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet” in method for ‘getParameters’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet” in method for ‘getDatasets’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet” in method for ‘boxplot’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet” in method for ‘corrPlot’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet” in method for ‘densityPlot’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet” Creating a new generic function for ‘meanSdPlot’ in package ‘Doscheda’ ** 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 (Doscheda)
Doscheda.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(Doscheda) > > test_check("Doscheda") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 9.687 0.776 13.400
Doscheda.Rcheck/Doscheda-Ex.timings
name | user | system | elapsed | |
corrPlot-methods | 4.427 | 0.289 | 10.702 | |
densityPlot-methods | 3.468 | 0.070 | 6.383 | |
doschedaData | 0.066 | 0.011 | 0.090 | |
fitModel-methods | 52.279 | 5.747 | 69.083 | |
getDatasets-methods | 0.000 | 0.000 | 0.001 | |
getFinal-methods | 0.001 | 0.001 | 0.001 | |
getInput-methods | 0.000 | 0.000 | 0.001 | |
getNorm-methods | 0.001 | 0.000 | 0.001 | |
getParameters-methods | 0.000 | 0.001 | 0.003 | |
makeReport | 0.001 | 0.000 | 0.001 | |
meanSdPlot-methods | 4.125 | 0.080 | 6.694 | |
pcaPlot-methods | 9.092 | 0.127 | 14.551 | |
processedExample | 0.130 | 0.013 | 0.164 | |
removePeptides-methods | 0.000 | 0.001 | 0.001 | |
replicatePlot-methods | 3.452 | 0.081 | 5.988 | |
runDoscheda | 45.629 | 0.272 | 54.142 | |
runNormalisation-methods | 4.862 | 2.202 | 9.772 | |
setData-methods | 0.978 | 1.767 | 3.013 | |
setParameters-methods | 0.003 | 0.003 | 0.006 | |
volcanoPlot-methods | 3.500 | 0.065 | 5.898 | |