Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:41:10 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 1625/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
qPLEXanalyzer 1.21.0 (landing page) Ashley Sawle
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the qPLEXanalyzer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qPLEXanalyzer.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: qPLEXanalyzer |
Version: 1.21.0 |
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:qPLEXanalyzer.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings qPLEXanalyzer_1.21.0.tar.gz |
StartedAt: 2024-03-28 08:36:25 -0000 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 08:42:19 -0000 (Thu, 28 Mar 2024) |
EllapsedTime: 353.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: qPLEXanalyzer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:qPLEXanalyzer.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings qPLEXanalyzer_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/qPLEXanalyzer.Rcheck’ * using R Under development (unstable) (2024-03-19 r86153) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘qPLEXanalyzer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘qPLEXanalyzer’ version ‘1.21.0’ * 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 ‘qPLEXanalyzer’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Updates to vignette to avoid build errors when attempting to connect to Uniprot * 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 loading without being on the library search path ... 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 ... NOTE convertToMSnset: no visible binding for global variable ‘SampleName’ corrPlot: no visible binding for global variable ‘X’ corrPlot: no visible binding for global variable ‘AddValues’ corrPlot: no visible binding for global variable ‘Cor’ corrPlot: no visible binding for global variable ‘Y’ corrPlot: no visible binding for global variable ‘CorTxt’ coveragePlot: no visible binding for global variable ‘Accessions’ coveragePlot: no visible binding for global variable ‘Sequences’ getContrastResults: no visible binding for global variable ‘B’ getContrastResults: no visible binding for global variable ‘AveExpr’ getContrastResults: no visible binding for global variable ‘logFC’ groupScaling: no visible binding for global variable ‘sInt’ groupScaling: no visible binding for global variable ‘meanscaledIntensity’ hierarchicalPlot: no visible binding for global variable ‘x’ hierarchicalPlot: no visible binding for global variable ‘y’ hierarchicalPlot: no visible binding for global variable ‘xend’ hierarchicalPlot: no visible binding for global variable ‘yend’ hierarchicalPlot: no visible binding for global variable ‘SampleName’ intensityBoxplot: no visible binding for global variable ‘Intensity’ intensityBoxplot: no visible binding for global variable ‘logInt’ intensityBoxplot: no visible binding for global variable ‘SampleName’ intensityPlot: no visible binding for global variable ‘Intensity’ intensityPlot: no visible binding for global variable ‘SampleName’ maVolPlot: no visible binding for global variable ‘group’ maVolPlot: no visible binding for global variable ‘adj.P.Val’ maVolPlot: no visible binding for global variable ‘GeneSymbol’ maVolPlot: no visible binding for global variable ‘SymbolLab’ mergePeptides: no visible binding for global variable ‘Accessions’ mergePeptides: no visible binding for global variable ‘Sequences’ mergePeptides: no visible binding for global variable ‘Seq_Acc’ mergePeptides: no visible global function definition for ‘where’ mergePeptides: no visible binding for global variable ‘Count’ mergeSites: no visible binding for global variable ‘Accessions’ mergeSites: no visible binding for global variable ‘Sites’ mergeSites: no visible binding for global variable ‘Type’ mergeSites: no visible binding for global variable ‘Sites_Acc’ mergeSites: no visible global function definition for ‘where’ mergeSites: no visible binding for global variable ‘Count’ peptideIntensityPlot: no visible binding for global variable ‘PeptideID’ peptideIntensityPlot: no visible binding for global variable ‘Intensity’ peptideIntensityPlot: no visible binding for global variable ‘Accessions’ peptideIntensityPlot: no visible binding for global variable ‘SampleName’ peptideIntensityPlot: no visible binding for global variable ‘logIntensity’ peptideIntensityPlot: no visible binding for global variable ‘Sequences’ peptideIntensityPlot: no visible binding for global variable ‘Modifications’ plotMeanVar: no visible binding for global variable ‘x’ plotMeanVar: no visible binding for global variable ‘y’ plotMeanVar: no visible binding for global variable ‘Mean’ plotMeanVar: no visible binding for global variable ‘Variance’ rliPlot: no visible binding for global variable ‘RowID’ rliPlot: no visible binding for global variable ‘Intensity’ rliPlot: no visible binding for global variable ‘logInt’ rliPlot: no visible binding for global variable ‘medianLogInt’ rliPlot: no visible binding for global variable ‘SampleName’ rliPlot: no visible binding for global variable ‘RLI’ summarizeIntensities: no visible binding for global variable ‘Accessions’ summarizeIntensities: no visible binding for global variable ‘Sequences’ summarizeIntensities: no visible global function definition for ‘where’ summarizeIntensities: no visible binding for global variable ‘Count’ Undefined global functions or variables: Accessions AddValues AveExpr B Cor CorTxt Count GeneSymbol Intensity Mean Modifications PeptideID RLI RowID SampleName Seq_Acc Sequences Sites Sites_Acc SymbolLab Type Variance X Y adj.P.Val group logFC logInt logIntensity meanscaledIntensity medianLogInt sInt where x xend y yend * 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 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 IRSnorm 6.323 0.196 6.532 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/qPLEXanalyzer.Rcheck/00check.log’ for details.
qPLEXanalyzer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL qPLEXanalyzer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’ * installing *source* package ‘qPLEXanalyzer’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to '==' Note: wrong number of arguments to '==' ** 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 (qPLEXanalyzer)
qPLEXanalyzer.Rcheck/qPLEXanalyzer-Ex.timings
name | user | system | elapsed | |
IRSnorm | 6.323 | 0.196 | 6.532 | |
assignColours | 0.265 | 0.004 | 0.269 | |
computeDiffStats | 0.611 | 0.012 | 0.624 | |
convertToMSnset | 1.290 | 0.084 | 1.377 | |
corrPlot | 1.063 | 0.011 | 1.077 | |
coveragePlot | 0.825 | 0.003 | 0.832 | |
getContrastResults | 0.616 | 0.016 | 0.633 | |
groupScaling | 0.288 | 0.015 | 0.304 | |
hierarchicalPlot | 0.387 | 0.020 | 0.408 | |
intensityBoxplot | 2.386 | 0.020 | 2.411 | |
intensityPlot | 1.171 | 0.024 | 1.197 | |
maVolPlot | 1.340 | 0.012 | 1.354 | |
mergePeptides | 0.792 | 0.004 | 0.797 | |
mergeSites | 0.252 | 0.000 | 0.252 | |
normalizeQuantiles | 0.268 | 0.008 | 0.276 | |
normalizeScaling | 0.286 | 0.000 | 0.287 | |
pcaPlot | 0.816 | 0.016 | 0.834 | |
peptideIntensityPlot | 0.799 | 0.008 | 0.809 | |
plotMeanVar | 0.771 | 0.008 | 0.781 | |
regressIntensity | 2.783 | 0.068 | 2.858 | |
rliPlot | 2.367 | 0.084 | 2.457 | |
rowScaling | 0.699 | 0.008 | 0.707 | |
summarizeIntensities | 0.501 | 0.000 | 0.502 | |