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CHECK report for proteoQC on tokay1

This page was generated on 2019-04-13 11:23:56 -0400 (Sat, 13 Apr 2019).

Package 1208/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
proteoQC 1.18.1
Bo Wen
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/proteoQC
Branch: RELEASE_3_8
Last Commit: bb59619
Last Changed Date: 2019-01-04 13:46:00 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: proteoQC
Version: 1.18.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proteoQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings proteoQC_1.18.1.tar.gz
StartedAt: 2019-04-13 04:43:30 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:48:11 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 281.1 seconds
RetCode: 0
Status:  OK  
CheckDir: proteoQC.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proteoQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings proteoQC_1.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/proteoQC.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 '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
* 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
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
labelRatio 5.27   0.09   26.33
chargeStat 5.09   0.08    5.27
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
labelRatio 5.75   0.01   29.06
chargeStat 5.47   0.05    5.52
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/proteoQC.Rcheck/00check.log'
for details.

Installation output

proteoQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/proteoQC_1.18.1.tar.gz && rm -rf proteoQC.buildbin-libdir && mkdir proteoQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=proteoQC.buildbin-libdir proteoQC_1.18.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL proteoQC_1.18.1.zip && rm proteoQC_1.18.1.tar.gz proteoQC_1.18.1.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
100 4558k  100 4558k    0     0  59.0M      0 --:--:-- --:--:-- --:--:-- 61.8M

install for i386

* installing *source* package 'proteoQC' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'proteoQC'
    finding HTML links ... done
    addSummaryChart                         html  
    calcMSQCMetrics                         html  
    chargeStat                              html  
    cntStat                                 html  
    combineRun                              html  
    createTargetDecoyDB                     html  
    getEnzyme                               html  
    getMods                                 html  
    labelRatio                              html  
    loadmsQCres                             html  
    msQCpipe                                html  
    plotBioRepVenn                          html  
    plotFractionIDResult                    html  
    plotMS1Error                            html  
    plotMS2Error                            html  
    plotMS2Error_obsolete                   html  
    plotSampleIDResultErrorBar              html  
    plotSampleVenn                          html  
    plotTechRepVenn                         html  
    print.msQCres                           html  
    proteinGroup                            html  
    reportHTML                              html  
    runTandem                               html  
    showEnzyme                              html  
    showMods                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'proteoQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'proteoQC' as proteoQC_1.18.1.zip
* DONE (proteoQC)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'proteoQC' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

proteoQC.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

> 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 -- Sat Apr 13 04:48:00 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 
   4.12    0.37    4.50

proteoQC.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

> 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 -- Sat Apr 13 04:48:06 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 
   4.75    0.28    5.03

Example timings

proteoQC.Rcheck/examples_i386/proteoQC-Ex.timings

nameusersystemelapsed
chargeStat5.090.085.27
labelRatio 5.27 0.0926.33
loadmsQCres0.020.032.14
msQCpipe000
print.msQCres0.090.040.12
proteinGroup0.000.001.17
reportHTML0.090.030.13
showEnzyme000
showMods000

proteoQC.Rcheck/examples_x64/proteoQC-Ex.timings

nameusersystemelapsed
chargeStat5.470.055.52
labelRatio 5.75 0.0129.06
loadmsQCres0.050.080.12
msQCpipe000
print.msQCres0.040.060.11
proteinGroup0.000.020.24
reportHTML0.060.050.11
showEnzyme000
showMods000