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This page was generated on 2022-04-13 12:07:09 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 tokay2


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 1500/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qPLEXanalyzer 1.12.1  (landing page)
Ashley Sawle
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/qPLEXanalyzer
git_branch: RELEASE_3_14
git_last_commit: 999e117
git_last_commit_date: 2022-03-16 10:34:06 -0400 (Wed, 16 Mar 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: qPLEXanalyzer
Version: 1.12.1
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qPLEXanalyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings qPLEXanalyzer_1.12.1.tar.gz
StartedAt: 2022-04-13 01:05:21 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 01:10:04 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 283.7 seconds
RetCode: 0
Status:   OK  
CheckDir: qPLEXanalyzer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qPLEXanalyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings qPLEXanalyzer_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/qPLEXanalyzer.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'qPLEXanalyzer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'qPLEXanalyzer' version '1.12.1'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-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/3.14/bioc/src/contrib/qPLEXanalyzer_1.12.1.tar.gz && rm -rf qPLEXanalyzer.buildbin-libdir && mkdir qPLEXanalyzer.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qPLEXanalyzer.buildbin-libdir qPLEXanalyzer_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL qPLEXanalyzer_1.12.1.zip && rm qPLEXanalyzer_1.12.1.tar.gz qPLEXanalyzer_1.12.1.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
 15 3893k   15  615k    0     0   996k      0  0:00:03 --:--:--  0:00:03  995k
 65 3893k   65 2536k    0     0  1566k      0  0:00:02  0:00:01  0:00:01 1566k
100 3893k  100 3893k    0     0  1822k      0  0:00:02  0:00:02 --:--:-- 1823k

install for i386

* 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
  converting help for package 'qPLEXanalyzer'
    finding HTML links ... done
    ER_ARID1A_KO_MCF7                       html  
    IRSnorm                                 html  
    finding level-2 HTML links ... done

    assignColours                           html  
    computeDiffStats                        html  
    convertToMSnset                         html  
    corrPlot                                html  
    coveragePlot                            html  
    exp2_Xlink                              html  
    exp3_OHT_ESR1                           html  
    getContrastResults                      html  
    groupScaling                            html  
    hierarchicalPlot                        html  
    human_anno                              html  
    intensityBoxplot                        html  
    intensityPlot                           html  
    maVolPlot                               html  
    mergePeptides                           html  
    mouse_anno                              html  
    normalizeQuantiles                      html  
    normalizeScaling                        html  
    pcaPlot                                 html  
    peptideIntensityPlot                    html  
    plotMeanVar                             html  
    qPLEXanalyzer-package                   html  
    regressIntensity                        html  
    rliPlot                                 html  
    rowScaling                              html  
    summarizeIntensities                    html  
** 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

install for x64

* installing *source* package 'qPLEXanalyzer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qPLEXanalyzer' as qPLEXanalyzer_1.12.1.zip
* DONE (qPLEXanalyzer)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'qPLEXanalyzer' successfully unpacked and MD5 sums checked

Tests output

qPLEXanalyzer.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 2.20.4 
  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 10 | SKIP 11 | PASS 156 ]

== Skipped tests ===============================================================
* On CRAN (11)

[ FAIL 0 | WARN 10 | SKIP 11 | PASS 156 ]
> 
> proc.time()
   user  system elapsed 
  24.81    1.01   25.81 

qPLEXanalyzer.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
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 2.20.4 
  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 10 | SKIP 11 | PASS 156 ]

== Skipped tests ===============================================================
* On CRAN (11)

[ FAIL 0 | WARN 10 | SKIP 11 | PASS 156 ]
> 
> proc.time()
   user  system elapsed 
  23.68    0.70   24.43 

Example timings

qPLEXanalyzer.Rcheck/examples_i386/qPLEXanalyzer-Ex.timings

nameusersystemelapsed
IRSnorm3.920.174.11
assignColours0.250.040.29
computeDiffStats0.750.080.83
convertToMSnset0.300.030.32
corrPlot0.690.040.72
coveragePlot0.730.010.75
getContrastResults0.990.051.03
groupScaling0.290.010.32
hierarchicalPlot0.360.000.36
intensityBoxplot1.000.031.03
intensityPlot0.990.000.98
maVolPlot1.110.021.13
mergePeptides0.700.020.72
normalizeQuantiles0.330.010.34
normalizeScaling0.310.000.31
pcaPlot0.770.000.76
peptideIntensityPlot0.710.030.75
plotMeanVar1.210.001.21
regressIntensity2.170.032.20
rliPlot1.780.031.81
rowScaling0.550.050.60
summarizeIntensities0.420.010.44

qPLEXanalyzer.Rcheck/examples_x64/qPLEXanalyzer-Ex.timings

nameusersystemelapsed
IRSnorm4.250.044.28
assignColours0.250.010.27
computeDiffStats0.530.050.58
convertToMSnset0.270.010.28
corrPlot0.620.040.66
coveragePlot1.220.011.23
getContrastResults0.530.020.55
groupScaling0.320.010.33
hierarchicalPlot0.390.000.39
intensityBoxplot1.110.051.16
intensityPlot1.390.051.43
maVolPlot1.200.011.22
mergePeptides0.640.020.66
normalizeQuantiles0.270.000.26
normalizeScaling0.250.010.27
pcaPlot0.700.020.72
peptideIntensityPlot0.660.010.67
plotMeanVar0.640.020.66
regressIntensity2.20.02.2
rliPlot1.660.031.69
rowScaling0.790.050.84
summarizeIntensities0.440.030.47