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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1631/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qPLEXanalyzer 1.24.0  (landing page)
Ashley Sawle
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/qPLEXanalyzer
git_branch: RELEASE_3_20
git_last_commit: 29217cb
git_last_commit_date: 2024-10-29 10:29:37 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for qPLEXanalyzer on kunpeng2

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.

raw results


Summary

Package: qPLEXanalyzer
Version: 1.24.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:qPLEXanalyzer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings qPLEXanalyzer_1.24.0.tar.gz
StartedAt: 2024-11-20 11:19:12 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 11:25:10 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 357.6 seconds
RetCode: 0
Status:   OK  
CheckDir: qPLEXanalyzer.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:qPLEXanalyzer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings qPLEXanalyzer_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/qPLEXanalyzer.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    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 ‘1.24.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
IRSnorm 5.398  0.168   5.577
* 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-3.20-bioc/meat/qPLEXanalyzer.Rcheck/00check.log’
for details.


Installation output

qPLEXanalyzer.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL qPLEXanalyzer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/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)

Tests output


Example timings

qPLEXanalyzer.Rcheck/qPLEXanalyzer-Ex.timings

nameusersystemelapsed
IRSnorm5.3980.1685.577
assignColours0.2630.0040.268
coefVar2.4350.0482.488
computeDiffStats0.5730.0160.590
convertToMSnset0.2370.0160.254
corrPlot1.1100.0081.121
coveragePlot0.8120.0000.814
getContrastResults1.7090.0081.720
groupScaling0.2990.0000.300
hierarchicalPlot0.3800.0000.382
intensityBoxplot1.4160.0441.463
intensityPlot1.1780.0201.200
maVolPlot1.3300.0041.337
mergePeptides0.8200.0040.825
mergeSites0.2480.0040.254
normalizeQuantiles0.2800.0000.281
normalizeScaling0.3110.0160.327
pcaPlot0.9900.0080.826
peptideIntensityPlot0.8380.0200.860
plotMeanVar0.8000.0030.806
regressIntensity2.8240.0392.868
rliPlot2.3260.0242.354
rowScaling0.7360.0040.742
summarizeIntensities0.4780.0120.492