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This page was generated on 2023-09-23 11:36:59 -0400 (Sat, 23 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4625
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4378
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4394
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 1600/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qPLEXanalyzer 1.18.0  (landing page)
Ashley Sawle
Snapshot Date: 2023-09-22 14:00:14 -0400 (Fri, 22 Sep 2023)
git_url: https://git.bioconductor.org/packages/qPLEXanalyzer
git_branch: RELEASE_3_17
git_last_commit: 011b364
git_last_commit_date: 2023-04-25 11:02:47 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for qPLEXanalyzer on merida1


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.

raw results


Summary

Package: qPLEXanalyzer
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qPLEXanalyzer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qPLEXanalyzer_1.18.0.tar.gz
StartedAt: 2023-09-23 06:41:18 -0400 (Sat, 23 Sep 2023)
EndedAt: 2023-09-23 06:47:53 -0400 (Sat, 23 Sep 2023)
EllapsedTime: 395.1 seconds
RetCode: 0
Status:   OK  
CheckDir: qPLEXanalyzer.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qPLEXanalyzer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qPLEXanalyzer_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/qPLEXanalyzer.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qPLEXanalyzer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qPLEXanalyzer’ version ‘1.18.0’
* 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 R 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
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          9.849  0.192  12.221
regressIntensity 4.987  0.038   6.194
rliPlot          4.100  0.089   5.266
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/qPLEXanalyzer.Rcheck/00check.log’
for details.



Installation output

qPLEXanalyzer.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL qPLEXanalyzer
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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)

Tests output


Example timings

qPLEXanalyzer.Rcheck/qPLEXanalyzer-Ex.timings

nameusersystemelapsed
IRSnorm 9.849 0.19212.221
assignColours0.4670.0220.599
computeDiffStats0.9750.0261.237
convertToMSnset0.4480.0130.571
corrPlot1.3840.0211.723
coveragePlot1.4340.0361.879
getContrastResults1.0420.0211.364
groupScaling1.0230.0161.300
hierarchicalPlot0.6710.0100.831
intensityBoxplot2.6680.0773.293
intensityPlot1.8330.0692.329
maVolPlot2.2990.0492.889
mergePeptides1.2840.0231.591
mergeSites0.4030.0110.509
normalizeQuantiles0.4260.0130.537
normalizeScaling0.4570.0150.574
pcaPlot1.5430.0261.940
peptideIntensityPlot1.3140.0241.661
plotMeanVar1.2910.0451.722
regressIntensity4.9870.0386.194
rliPlot4.1000.0895.266
rowScaling1.3530.0171.678
summarizeIntensities0.7900.0150.977