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 12:05 -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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:qPLEXanalyzer.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings qPLEXanalyzer_1.24.0.tar.gz |
StartedAt: 2024-12-20 04:54:49 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:00:20 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 331.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: qPLEXanalyzer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:qPLEXanalyzer.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings qPLEXanalyzer_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/qPLEXanalyzer.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'qPLEXanalyzer/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'qPLEXanalyzer' version '1.24.0' * 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 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 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/qPLEXanalyzer.Rcheck/00check.log' for details.
qPLEXanalyzer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL qPLEXanalyzer ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 | 4.58 | 0.10 | 4.67 | |
assignColours | 0.24 | 0.03 | 0.27 | |
coefVar | 0.98 | 0.00 | 0.98 | |
computeDiffStats | 0.66 | 0.01 | 0.67 | |
convertToMSnset | 0.22 | 0.02 | 0.24 | |
corrPlot | 0.89 | 0.03 | 1.01 | |
coveragePlot | 0.78 | 0.03 | 0.91 | |
getContrastResults | 0.59 | 0.08 | 0.67 | |
groupScaling | 0.36 | 0.00 | 0.36 | |
hierarchicalPlot | 0.32 | 0.02 | 0.33 | |
intensityBoxplot | 1.93 | 0.04 | 1.98 | |
intensityPlot | 0.96 | 0.05 | 1.00 | |
maVolPlot | 1.21 | 0.06 | 1.29 | |
mergePeptides | 0.71 | 0.03 | 0.73 | |
mergeSites | 0.22 | 0.00 | 0.22 | |
normalizeQuantiles | 0.20 | 0.05 | 0.25 | |
normalizeScaling | 0.30 | 0.05 | 0.35 | |
pcaPlot | 0.76 | 0.04 | 0.81 | |
peptideIntensityPlot | 0.69 | 0.02 | 0.70 | |
plotMeanVar | 0.70 | 0.02 | 1.00 | |
regressIntensity | 3.39 | 0.03 | 3.42 | |
rliPlot | 1.68 | 0.13 | 1.80 | |
rowScaling | 0.51 | 0.03 | 0.54 | |
summarizeIntensities | 0.33 | 0.01 | 0.35 | |