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This page was generated on 2022-06-24 11:07:01 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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

CHECK results for qPLEXanalyzer on palomino4


To the developers/maintainers of the qPLEXanalyzer package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1521/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qPLEXanalyzer 1.15.0  (landing page)
Ashley Sawle
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/qPLEXanalyzer
git_branch: master
git_last_commit: d74a8ee
git_last_commit_date: 2022-04-26 11:49:51 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: qPLEXanalyzer
Version: 1.15.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qPLEXanalyzer.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings qPLEXanalyzer_1.15.0.tar.gz
StartedAt: 2022-06-24 04:43:29 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:46:37 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 187.9 seconds
RetCode: 0
Status:   OK  
CheckDir: qPLEXanalyzer.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qPLEXanalyzer.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings qPLEXanalyzer_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/qPLEXanalyzer.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'qPLEXanalyzer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'qPLEXanalyzer' version '1.15.0'
* 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 ... OK
* 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 'phosseqid'
mergePeptides: no visible global function definition for 'where'
mergePeptides: 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 Sequences SymbolLab
  Variance X Y adj.P.Val group logFC logInt logIntensity
  meanscaledIntensity medianLogInt phosseqid 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 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.16-bioc/meat/qPLEXanalyzer.Rcheck/00check.log'
for details.



Installation output

qPLEXanalyzer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/qPLEXanalyzer_1.15.0.tar.gz && rm -rf qPLEXanalyzer.buildbin-libdir && mkdir qPLEXanalyzer.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qPLEXanalyzer.buildbin-libdir qPLEXanalyzer_1.15.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL qPLEXanalyzer_1.15.0.zip && rm qPLEXanalyzer_1.15.0.tar.gz qPLEXanalyzer_1.15.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3893k  100 3893k    0     0  11.4M      0 --:--:-- --:--:-- --:--:-- 11.4M
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'qPLEXanalyzer' as qPLEXanalyzer_1.15.0.zip
* DONE (qPLEXanalyzer)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'qPLEXanalyzer' successfully unpacked and MD5 sums checked

Tests output

qPLEXanalyzer.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(vdiffr)
> library(qPLEXanalyzer)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth


This is MSnbase version 2.23.0 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:base':

    trimws

> 
> options(lifecycle_verbosity = "warning")
> test_check("qPLEXanalyzer")
[ FAIL 0 | WARN 0 | SKIP 11 | PASS 156 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (11)

[ FAIL 0 | WARN 0 | SKIP 11 | PASS 156 ]
> 
> proc.time()
   user  system elapsed 
  22.23    0.82   23.39 

Example timings

qPLEXanalyzer.Rcheck/qPLEXanalyzer-Ex.timings

nameusersystemelapsed
IRSnorm3.730.073.82
assignColours0.220.020.23
computeDiffStats0.520.020.58
convertToMSnset0.220.000.21
corrPlot0.660.010.68
coveragePlot0.680.020.70
getContrastResults0.990.000.98
groupScaling0.260.000.27
hierarchicalPlot0.300.010.31
intensityBoxplot1.140.031.17
intensityPlot1.380.071.44
maVolPlot1.100.071.19
mergePeptides0.650.020.65
normalizeQuantiles0.250.000.25
normalizeScaling0.250.000.25
pcaPlot0.950.000.96
peptideIntensityPlot0.650.000.65
plotMeanVar1.150.021.16
regressIntensity2.070.012.09
rliPlot1.460.111.57
rowScaling0.450.050.50
summarizeIntensities0.360.000.36