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CHECK report for msPurity on merida2

This page was generated on 2018-10-17 08:56:37 -0400 (Wed, 17 Oct 2018).

Package 956/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
msPurity 1.6.2
Thomas N. Lawson
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/msPurity
Branch: RELEASE_3_7
Last Commit: a9e6c12
Last Changed Date: 2018-06-10 09:48:41 -0400 (Sun, 10 Jun 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: msPurity
Version: 1.6.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msPurity.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msPurity_1.6.2.tar.gz
StartedAt: 2018-10-16 22:49:04 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 23:00:42 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 697.7 seconds
RetCode: 0
Status:  OK 
CheckDir: msPurity.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msPurity.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msPurity_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/msPurity.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘msPurity/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘msPurity’ version ‘1.6.2’
* 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 ‘msPurity’ 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 ... NOTE
Package in Depends field not imported from: ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CV: no visible global function definition for ‘sd’
Getfiles: no visible global function definition for ‘fix’
assessPuritySingle: no visible binding for global variable ‘parallel’
averageCluster: no visible global function definition for ‘sd’
averageCluster: no visible global function definition for ‘median’
averageSpectraSingle: no visible binding for global variable ‘scanid’
covar: no visible global function definition for ‘sd’
dimsPredictPuritySingle: no visible global function definition for
  ‘read.csv’
dimsPredictPuritySingleMz: no visible global function definition for
  ‘png’
dimsPredictPuritySingleMz: no visible binding for global variable
  ‘mtchi’
dimsPredictPuritySingleMz: no visible binding for global variable
  ‘alli’
dimsPredictPuritySingleMz: no visible global function definition for
  ‘points’
dimsPredictPuritySingleMz: no visible binding for global variable
  ‘mtch’
dimsPredictPuritySingleMz: no visible global function definition for
  ‘text’
dimsPredictPuritySingleMz: no visible global function definition for
  ‘dev.off’
dimsPredictPuritySingleMz: no visible global function definition for
  ‘median’
dimsPredictPuritySingleMz: no visible global function definition for
  ‘sd’
export_2_sqlite: no visible global function definition for ‘read.table’
export_2_sqlite: no visible global function definition for ‘read.csv’
get_topn: no visible binding for global variable ‘topn’
groupPeaksEx: no visible binding for global variable ‘median’
iwNormGauss: no visible global function definition for ‘dnorm’
iwNormGauss: no visible global function definition for ‘approxfun’
iwNormQE.5: no visible global function definition for ‘approxfun’
iwNormRcosine: no visible global function definition for ‘approxfun’
linearPurity: no visible global function definition for ‘approxfun’
medGroup: no visible binding for global variable ‘median’
median_match_results: no visible global function definition for
  ‘median’
msfrProcess: no visible global function definition for ‘read.csv’
performHc: no visible global function definition for ‘dist’
performHc: no visible global function definition for ‘as.dist’
plotPurity: no visible global function definition for ‘png’
plotPurity: no visible binding for global variable ‘idx’
plotPurity: no visible binding for global variable ‘purity’
plotPurity: no visible binding for global variable ‘variable’
plotPurity: no visible global function definition for ‘dev.off’
plotPurity: no visible global function definition for ‘write.csv’
pp4file: no visible global function definition for ‘png’
pp4file: no visible global function definition for ‘plot’
pp4file: no visible global function definition for ‘lines’
pp4file: no visible global function definition for ‘legend’
pp4file: no visible global function definition for ‘abline’
pp4file: no visible global function definition for ‘dev.off’
pp4file: no visible global function definition for ‘median’
predictPurityLCMSloop: no visible global function definition for
  ‘median’
predictPurityLCMSloop : <anonymous>: no visible global function
  definition for ‘na.omit’
predictPurityLCMSloop : <anonymous>: no visible global function
  definition for ‘median’
predictPurityLCMSloop : <anonymous>: no visible global function
  definition for ‘sd’
purityA: no visible binding for global variable ‘i’
removeIsotopes: no visible global function definition for ‘write.csv’
rsde: no visible global function definition for ‘sd’
snrFilter: no visible global function definition for ‘median’
stde: no visible global function definition for ‘sd’
stderror: no visible global function definition for ‘sd’
xcmsGroupPurity: no visible binding for global variable ‘median’
xcmsGroupPurity: no visible global function definition for ‘median’
averageSpectra,purityD: no visible binding for global variable ‘i’
subtract,purityD: no visible binding for global variable ‘i’
validate,purityA: no visible global function definition for ‘head’
writeOut,purityD: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  abline alli approxfun as.dist dev.off dist dnorm fix head i idx
  legend lines median mtch mtchi na.omit parallel plot png points
  purity read.csv read.table scanid sd text topn variable write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "legend", "lines", "plot", "points",
             "text")
  importFrom("stats", "approxfun", "as.dist", "dist", "dnorm", "median",
             "na.omit", "sd")
  importFrom("utils", "fix", "head", "read.csv", "read.table",
             "write.csv")
to your NAMESPACE file.
* 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
spectral_matching                95.371  2.594  99.373
frag4feature-purityA-method      64.224  1.079  66.520
dimsPredictPurity-purityD-method 48.833  1.684  51.100
assessPuritySingle               15.597  0.115  15.815
purityX                          14.367  1.136  15.639
purityA                          13.038  0.170  13.297
subtract-purityD-method           8.858  1.744  10.710
groupPeaks-purityD-method         8.035  1.679   9.794
groupPeaksEx                      6.251  1.784   8.113
averageSpectra-purityD-method     4.947  1.738   6.721
filterp-purityD-method            4.553  1.718   6.305
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/msPurity.Rcheck/00check.log’
for details.



Installation output

msPurity.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL msPurity
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘msPurity’ ...
** 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 (msPurity)

Tests output

msPurity.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(msPurity)
Loading required package: Rcpp
> Sys.setenv("R_TESTS" = "")
> test_check("msPurity")
[1] "########################################################"
[1] "## Checking LCMS based class and functions            ##"
[1] "########################################################"
[1] 6
[1] "########################################################"
[1] "## Checking file list function                        ##"
[1] "########################################################"
[1] "=== check for using csv ==="
[1] "=== check for using mzML ==="
[1] "########################################################"
[1] "## Check average spectra (function only)              ##"
[1] "########################################################"
[1] "=== check single core ==="
[1] "=== check simple clustering ==="
[1] "=== check using MsFileReader output (median SNR thres) ==="
snmeth: median[1] "=== check using MsFileReader output (precalc SNR thres) ==="
snmeth: precalc[1] "########################################################"
[1] "## Check mz subtraction (function only)               ##"
[1] "########################################################"
[1] "########################################################"
[1] "## Check predict purity (function only)               ##"
[1] "########################################################"
[1] "=== Check predicted purity for mzML files ==="
[1] "########################################################"
[1] "## Check groupPeaks (function only)               ##"
[1] "########################################################"
[1] "=== check single core ==="
[1] "########################################################"
[1] "## Check mzML Workflow                                ##"
[1] "########################################################"
[1] "averaging spectra"
[1] "filtering spectra"
[1] "subtracting"
[1] "purity prediction"
[1] "########################################################"
[1] "## Checking LCMS based class and functions            ##"
[1] "########################################################"
[1] 4
[1] "########################################################"
[1] "## Checking pcalc functions                           ##"
[1] "########################################################"
[1] "########################################################"
[1] "## Spectral matching functions                        ##"
[1] "########################################################"
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 86 SKIPPED: 0 FAILED: 0
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
305.774  12.487 322.003 

Example timings

msPurity.Rcheck/msPurity-Ex.timings

nameusersystemelapsed
Getfiles0.0070.0010.007
assessPuritySingle15.597 0.11515.815
averageSpectra-purityD-method4.9471.7386.721
averageSpectraSingle2.2641.0913.373
dimsPredictPurity-purityD-method48.833 1.68451.100
dimsPredictPuritySingle0.0610.0010.063
filterp-purityD-method4.5531.7186.305
frag4feature-purityA-method64.224 1.07966.520
getP-purityD-method0.0190.0020.021
get_additional_mzml_meta0.0320.0010.033
groupPeaks-purityD-method8.0351.6799.794
groupPeaksEx6.2511.7848.113
initialize-purityD-method0.0040.0010.005
iwNormGauss0.0050.0000.005
iwNormQE.50.0050.0010.005
iwNormRcosine0.0030.0000.003
pcalc0.0080.0010.009
purityA13.038 0.17013.297
purityD-class0.0050.0010.006
purityX14.367 1.13615.639
spectral_matching95.371 2.59499.373
subtract-purityD-method 8.858 1.74410.710
subtractMZ0.0010.0000.002