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BioC 3.5: CHECK report for proteoQC on veracruz2

This page was generated on 2017-08-16 13:32:03 -0400 (Wed, 16 Aug 2017).

Package 1023/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
proteoQC 1.12.3
Bo Wen
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/proteoQC
Last Changed Rev: 129232 / Revision: 131943
Last Changed Date: 2017-04-27 15:40:20 -0400 (Thu, 27 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: proteoQC
Version: 1.12.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings proteoQC_1.12.3.tar.gz
StartedAt: 2017-08-16 06:47:49 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 06:51:02 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 193.5 seconds
RetCode: 0
Status:  OK 
CheckDir: proteoQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings proteoQC_1.12.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/proteoQC.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.12.3’
* 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 ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    extdata   3.9Mb
* 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 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
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
labelRatio 18.686  0.220  37.355
chargeStat 17.376  0.101  17.909
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/proteoQC.Rcheck/00check.log’
for details.


proteoQC.Rcheck/00install.out:

* installing *source* package ‘proteoQC’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (proteoQC)

proteoQC.Rcheck/proteoQC-Ex.timings:

nameusersystemelapsed
chargeStat17.376 0.10117.909
labelRatio18.686 0.22037.355
loadmsQCres0.0570.0440.101
msQCpipe0.0010.0000.001
print.msQCres0.0460.0250.072
proteinGroup0.5370.0540.257
reportHTML0.0440.0240.070
showEnzyme0.0030.0010.003
showMods0.0020.0000.003