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BioC 3.5: CHECK report for msPurity on toluca2

This page was generated on 2017-04-23 14:41:43 -0400 (Sun, 23 Apr 2017).

Package 860/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
msPurity 1.1.1
Thomas N. Lawson
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msPurity
Last Changed Rev: 125830 / Revision: 129046
Last Changed Date: 2017-01-10 12:32:59 -0500 (Tue, 10 Jan 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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: msPurity
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings msPurity_1.1.1.tar.gz
StartedAt: 2017-04-23 07:06:02 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 07:11:58 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 356.0 seconds
RetCode: 0
Status:  OK 
CheckDir: msPurity.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings msPurity_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/msPurity.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 loading without being on the library search path ... 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’
get_interp_purity: possible error in splinePurity(rowi, roi_scns,
  minoff, maxoff, ppm, mostIntense, scanids, plotP, plotdir, isotopes,
  im): unused arguments (isotopes, im)
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’
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’
purityX: no visible binding for global variable ‘median’
purityX: no visible global function definition for ‘median’
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’
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 scanid sd text 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", "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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
dimsPredictPurity-purityD-method 54.079  1.533  56.177
frag4feature-purityA-method      39.954  0.614  46.320
assessPuritySingle               16.097  0.094  16.509
purityA                          15.303  0.151  15.866
subtract-purityD-method           7.322  1.364   9.932
groupPeaks-purityD-method         6.272  1.485   7.818
purityX                           6.781  0.525  15.278
groupPeaksEx                      4.932  1.488   7.283
averageSpectra-purityD-method     4.563  1.337   5.959
filterp-purityD-method            3.869  1.438   5.368
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/msPurity.Rcheck/00check.log’
for details.


msPurity.Rcheck/00install.out:

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

msPurity.Rcheck/msPurity-Ex.timings:

nameusersystemelapsed
Getfiles0.0070.0000.008
assessPuritySingle16.097 0.09416.509
averageSpectra-purityD-method4.5631.3375.959
averageSpectraSingle1.9000.6762.592
dimsPredictPurity-purityD-method54.079 1.53356.177
dimsPredictPuritySingle0.0750.0020.080
filterp-purityD-method3.8691.4385.368
frag4feature-purityA-method39.954 0.61446.320
getP-purityD-method0.0040.0000.005
groupPeaks-purityD-method6.2721.4857.818
groupPeaksEx4.9321.4887.283
initialize-purityD-method0.0040.0010.005
pcalc0.0070.0000.007
purityA15.303 0.15115.866
purityD-class0.0040.0000.004
purityX 6.781 0.52515.278
subtract-purityD-method7.3221.3649.932
subtractMZ0.0010.0000.001