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 12:04 -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 1631/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
qPLEXanalyzer 1.24.0 (landing page) Ashley Sawle
| 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 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. |
Package: qPLEXanalyzer |
Version: 1.24.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:qPLEXanalyzer.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings qPLEXanalyzer_1.24.0.tar.gz |
StartedAt: 2024-12-20 04:28:12 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:32:56 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 284.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: qPLEXanalyzer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:qPLEXanalyzer.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings qPLEXanalyzer_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/qPLEXanalyzer.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘qPLEXanalyzer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘qPLEXanalyzer’ version ‘1.24.0’ * 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 coefVar: no visible binding for global variable ‘SampleName’ coefVar: no visible binding for global variable ‘CV’ coefVar: no visible binding for global variable ‘cum_sum’ coefVar: no visible binding for global variable ‘fraction’ 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 CV 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 cum_sum fraction 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/qPLEXanalyzer.Rcheck/00check.log’ for details.
qPLEXanalyzer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL qPLEXanalyzer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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 | 3.376 | 0.145 | 3.520 | |
assignColours | 0.221 | 0.023 | 0.246 | |
coefVar | 1.716 | 0.056 | 1.771 | |
computeDiffStats | 0.433 | 0.007 | 0.440 | |
convertToMSnset | 0.217 | 0.003 | 0.221 | |
corrPlot | 0.691 | 0.006 | 0.697 | |
coveragePlot | 0.603 | 0.014 | 0.616 | |
getContrastResults | 1.283 | 0.064 | 1.346 | |
groupScaling | 0.245 | 0.003 | 0.248 | |
hierarchicalPlot | 0.273 | 0.005 | 0.278 | |
intensityBoxplot | 0.907 | 0.032 | 0.939 | |
intensityPlot | 0.79 | 0.02 | 0.81 | |
maVolPlot | 0.919 | 0.025 | 0.944 | |
mergePeptides | 0.531 | 0.004 | 0.534 | |
mergeSites | 0.213 | 0.007 | 0.218 | |
normalizeQuantiles | 0.260 | 0.003 | 0.265 | |
normalizeScaling | 0.235 | 0.003 | 0.238 | |
pcaPlot | 0.593 | 0.019 | 0.612 | |
peptideIntensityPlot | 0.648 | 0.014 | 0.661 | |
plotMeanVar | 0.551 | 0.032 | 0.583 | |
regressIntensity | 1.848 | 0.042 | 1.890 | |
rliPlot | 1.531 | 0.024 | 1.555 | |
rowScaling | 0.467 | 0.005 | 0.472 | |
summarizeIntensities | 0.365 | 0.003 | 0.368 | |