Package: proteoQC

Version: 1.18.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:proteoQC.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings proteoQC_1.18.1.tar.gz

StartedAt: 2019-04-16 02:14:58 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:17:27 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 148.3 seconds

RetCode: 0

Status:  OK

CheckDir: proteoQC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:proteoQC.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings proteoQC_1.18.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/proteoQC.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘proteoQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proteoQC’ version ‘1.18.1’
* 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 ‘proteoQC’ 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
calcMSQCMetrics : <anonymous>: warning in readMSData(x, msLevel = 1):
  partial argument match of 'msLevel' to 'msLevel.'
calcMSQCMetrics : <anonymous>: warning in readMSData(x, msLevel = 2):
  partial argument match of 'msLevel' to 'msLevel.'
addSummaryChart: no visible binding for global variable ‘peplength’
addSummaryChart: no visible binding for global variable ‘..count..’
addSummaryChart: no visible binding for global variable ‘delta’
chargeStat: no visible global function definition for ‘readMgfData’
chargeStat: no visible global function definition for ‘precursorCharge’
ggplot.RT: no visible binding for global variable ‘x’
ggplot.RT: no visible binding for global variable ‘y’
ggplot.RT: no visible binding for global variable ‘techRep’
ggplot.RT: no visible binding for global variable ‘bioRep’
labelRatio: no visible global function definition for ‘readMgfData’
labelRatio: no visible binding for global variable ‘iTRAQ4’
labelRatio: no visible binding for global variable ‘iTRAQ8’
labelRatio: no visible binding for global variable ‘TMT6’
labelRatio: no visible binding for global variable ‘TMT10’
labelRatio: no visible global function definition for ‘exprs’
labelRatio: no visible global function definition for ‘quantify’
labelRatio: no visible binding for global variable ‘Tag’
labelRatio: no visible binding for global variable ‘Intensity’
labelRatio: no visible binding for global variable ‘ratio’
labelRatio: no visible binding for global variable ‘label’
msQC.barplot: no visible binding for global variable ‘x’
msQC.barplot: no visible binding for global variable ‘y’
msQC.barplot: no visible binding for global variable ‘label’
plotBioRepVenn : <anonymous>: no visible global function definition for
  ‘grid.draw’
plotMS1Count: no visible binding for global variable ‘bioRep’
plotMS1Count: no visible binding for global variable ‘techRep’
plotMS1Count: no visible binding for global variable ‘fraction’
plotMS1Count: no visible binding for global variable ‘MS1QC’
plotMS1CountErrorBar: no visible binding for global variable ‘bioRep’
plotMS1CountErrorBar: no visible binding for global variable ‘techRep’
plotMS1CountErrorBar: no visible binding for global variable ‘fraction’
plotMS1CountErrorBar: no visible binding for global variable ‘MS1QC’
plotMS1CountErrorBar: no visible binding for global variable ‘val’
plotMS1CountErrorBar: no visible binding for global variable ‘se’
plotMS1Error: no visible binding for '<<-' assignment to ‘curenv’
plotMS1Error: no visible binding for global variable ‘bioRep’
plotMS1Error: no visible binding for global variable ‘techRep’
plotMS1Error: no visible binding for global variable ‘fraction’
plotMS1Error: no visible binding for global variable ‘peptide_summary’
plotMS1Error: no visible binding for global variable ‘curenv’
plotMS1Error : <anonymous>: no visible binding for global variable
  ‘curenv’
plotMS1IonCount: no visible binding for global variable ‘bioRep’
plotMS1IonCount: no visible binding for global variable ‘techRep’
plotMS1IonCount: no visible binding for global variable ‘fraction’
plotMS1IonCount: no visible binding for global variable ‘MS1QC’
plotMS1PeaksCount: no visible binding for global variable ‘bioRep’
plotMS1PeaksCount: no visible binding for global variable ‘techRep’
plotMS1PeaksCount: no visible binding for global variable ‘fraction’
plotMS1PeaksCount: no visible binding for global variable ‘MS1QC’
plotMS1TIC: no visible binding for global variable ‘bioRep’
plotMS1TIC: no visible binding for global variable ‘techRep’
plotMS1TIC: no visible binding for global variable ‘fraction’
plotMS1TIC: no visible binding for global variable ‘MS1QC’
plotMS1boxplot: no visible binding for global variable ‘bioRep’
plotMS1boxplot: no visible binding for global variable ‘techRep’
plotMS1boxplot: no visible binding for global variable ‘fraction’
plotMS1boxplot: no visible binding for global variable ‘MS1QC’
plotMS2Error: no visible binding for global variable ‘bioRep’
plotMS2Error: no visible binding for global variable ‘techRep’
plotMS2Error: no visible binding for global variable ‘fraction’
plotMS2Error: no visible binding for global variable ‘V1’
plotMS2Error: no visible binding for global variable ‘V2’
plotMS2Error: no visible binding for global variable ‘V3’
plotMS2Error: no visible binding for global variable ‘V4’
plotMS2Error: no visible binding for global variable ‘V5’
plotMS2Error_obsolete: no visible binding for global variable ‘bioRep’
plotMS2Error_obsolete: no visible binding for global variable ‘techRep’
plotMS2Error_obsolete: no visible binding for global variable
  ‘fraction’
plotMS2Error_obsolete: no visible binding for global variable
  ‘peptide_summary’
plotMS2PeakFreq: no visible binding for global variable ‘bioRep’
plotMS2PeakFreq: no visible binding for global variable ‘techRep’
plotMS2PeakFreq: no visible binding for global variable ‘fraction’
plotMS2PeakFreq: no visible binding for global variable ‘MS2QC’
plotMS2boxplot: no visible binding for global variable ‘bioRep’
plotMS2boxplot: no visible binding for global variable ‘techRep’
plotMS2boxplot: no visible binding for global variable ‘fraction’
plotMS2boxplot: no visible binding for global variable ‘MS2QC’
plotSampleIDResultErrorBar: no visible binding for global variable
  ‘fraction’
plotSampleIDResultErrorBar: no visible binding for global variable
  ‘val’
plotSampleIDResultErrorBar: no visible binding for global variable ‘se’
plotSampleVenn: no visible global function definition for ‘grid.draw’
plotTechRepVenn : <anonymous>: no visible global function definition
  for ‘grid.draw’
qcHist: no visible binding for global variable ‘error’
qcHist: no visible binding for global variable ‘techRep’
qcHist: no visible binding for global variable ‘bioRep’
qcHist2: no visible binding for global variable ‘error’
qcHist2: no visible binding for global variable ‘fractile’
Undefined global functions or variables:
  ..count.. Intensity MS1QC MS2QC TMT10 TMT6 Tag V1 V2 V3 V4 V5 bioRep
  curenv delta error exprs fractile fraction grid.draw iTRAQ4 iTRAQ8
  label peplength peptide_summary precursorCharge quantify ratio
  readMgfData se techRep val x y
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
labelRatio 66.252  0.884  22.818
chargeStat  8.028  0.048   8.151
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/proteoQC.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL proteoQC
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘proteoQC’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (proteoQC)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> BiocGenerics:::testPackage("proteoQC")

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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")'.


Attaching package: 'S4Vectors'

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

    expand.grid


This is MSnbase version 2.8.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws



RUNIT TEST PROTOCOL -- Tue Apr 16 02:17:23 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
proteoQC RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  4.944   0.132   5.078 

name	user	system	elapsed
chargeStat	8.028	0.048	8.151
labelRatio	66.252	0.884	22.818
loadmsQCres	0.056	0.020	0.128
msQCpipe	0	0	0
print.msQCres	0.068	0.016	0.085
proteinGroup	0.552	0.068	0.543
reportHTML	0.104	0.016	0.120
showEnzyme	0.004	0.000	0.135
showMods	0.004	0.000	0.002