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BioC 3.5: CHECK report for RMassBank on veracruz2

This page was generated on 2017-08-16 13:30:28 -0400 (Wed, 16 Aug 2017).

Package 1125/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RMassBank 2.4.0
RMassBank at Eawag
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/RMassBank
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 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: RMassBank
Version: 2.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RMassBank_2.4.0.tar.gz
StartedAt: 2017-08-16 07:36:49 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 07:39:35 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 165.5 seconds
RetCode: 0
Status:  OK 
CheckDir: RMassBank.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RMassBank_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RMassBank.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 ‘RMassBank/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RMassBank’ version ‘2.4.0’
* package encoding: UTF-8
* 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 ‘RMassBank’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.findPattern: no visible global function definition for
  ‘capture.output’
.get.mol2formula: no visible global function definition for
  ‘capture.output’
.pubChemOnline: no visible global function definition for ‘URLencode’
addPeaks: no visible global function definition for ‘read.csv’
analyzeMsMs.formula.optimized: no visible binding for global variable
  ‘occurrenceMatrix’
checkIsotopes: no visible global function definition for ‘data’
checkIsotopes : <anonymous> : <anonymous>: no visible global function
  definition for ‘points’
createSpecsFromPeaklists: no visible global function definition for
  ‘read.csv’
deprofile.spline : <anonymous>: no visible global function definition
  for ‘smooth.spline’
deprofile.spline : <anonymous>: no visible global function definition
  for ‘predict’
findEIC: no visible global function definition for ‘predict’
findMsMsHRperxcms.direct : getRT : <anonymous>: no visible global
  function definition for ‘median’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘capture.output’
gatherSpectrum: no visible global function definition for
  ‘packageVersion’
getCSID: no visible global function definition for ‘URLencode’
getCactus: no visible global function definition for ‘URLencode’
getCtsKey: no visible global function definition for ‘URLencode’
getMolecule: no visible global function definition for ‘capture.output’
getPcCHEBI: no visible global function definition for ‘URLencode’
getPcIUPAC: no visible global function definition for ‘URLencode’
getPcId: no visible global function definition for ‘URLencode’
getPcInchiKey: no visible global function definition for ‘URLencode’
getPcSDF: no visible global function definition for ‘URLencode’
getPcSynonym: no visible global function definition for ‘URLencode’
loadInfolist: no visible global function definition for ‘read.csv’
loadInfolist: no visible global function definition for ‘read.csv2’
loadList: no visible global function definition for ‘read.csv’
loadList: no visible global function definition for ‘read.csv2’
makeMollist: no visible global function definition for ‘write.table’
makeRecalibration: no visible global function definition for ‘par’
mbWorkflow: no visible global function definition for ‘write.csv’
msmsRead: no visible global function definition for ‘read.csv’
msmsRead.RAW : getRT : <anonymous>: no visible global function
  definition for ‘median’
msmsRead.RAW: no visible global function definition for
  ‘capture.output’
msmsRead.ticms2: no visible global function definition for ‘read.csv’
msmsRead.ticms2: no visible global function definition for
  ‘c.msmsWSspecs’
newStep2WorkFlow: no visible global function definition for ‘read.csv’
parseMassBank: no visible binding for global variable ‘type.convert’
parseMassBank: no visible global function definition for
  ‘flush.console’
plotMbWorkspaces: no visible global function definition for ‘points’
plotRecalibration: no visible global function definition for ‘par’
plotRecalibration.direct: no visible global function definition for
  ‘predict’
plotRecalibration.direct: no visible global function definition for
  ‘lines’
plotRecalibration.direct: no visible global function definition for
  ‘heat.colors’
processProblematicPeaks: no visible global function definition for
  ‘write.csv’
progressBarHook: no visible global function definition for
  ‘txtProgressBar’
progressBarHook: no visible global function definition for
  ‘setTxtProgressBar’
recalibrate.identity: no visible global function definition for ‘lm’
recalibrate.linear: no visible global function definition for ‘lm’
recalibrate.loess: no visible global function definition for ‘loess’
recalibrate.mean: no visible global function definition for ‘lm’
recalibrateSingleSpec: no visible global function definition for
  ‘predict’
toRMB : <anonymous>: no visible global function definition for ‘median’
show,mbWorkspace: no visible global function definition for ‘str’
Undefined global functions or variables:
  URLencode c.msmsWSspecs capture.output data flush.console heat.colors
  lines lm loess median occurrenceMatrix packageVersion par points
  predict read.csv read.csv2 setTxtProgressBar smooth.spline str
  txtProgressBar type.convert write.csv write.table
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "lines", "par", "points")
  importFrom("stats", "lm", "loess", "median", "predict",
             "smooth.spline")
  importFrom("utils", "URLencode", "capture.output", "data",
             "flush.console", "packageVersion", "read.csv", "read.csv2",
             "setTxtProgressBar", "str", "txtProgressBar",
             "type.convert", "write.csv", "write.table")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/RMassBank.Rcheck/00check.log’
for details.


RMassBank.Rcheck/00install.out:

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

RMassBank.Rcheck/RMassBank-Ex.timings:

nameusersystemelapsed
CTS.externalIdSubset0.0010.0000.001
CTS.externalIdTypes0.0010.0010.001
RmbDefaultSettings0.0070.0010.007
add.formula0.0420.0000.042
addMB0.0000.0000.001
addPeaks0.0000.0000.001
addPeaksManually0.0010.0000.001
aggregateSpectra0.0010.0000.001
analyzeMsMs0.0010.0000.000
annotator.default0.0010.0000.000
archiveResults0.0110.0010.011
cleanElnoise000
combineMultiplicities0.0010.0010.001
compileRecord0.0010.0000.001
createMolfile0.0010.0000.001
dbe0.0010.0000.000
deprofile0.0010.0000.001
exportMassbank000
filterLowaccResults0.0010.0000.001
filterMultiplicity000
filterPeakSatellites0.0000.0000.001
filterPeaksMultiplicity0.0000.0000.001
findMass0.9840.0480.492
findMsMsHR0.0010.0000.001
findMsMsHRperxcms0.0000.0000.001
findMz0.0010.0000.001
findMz.formula0.2210.0010.227
findProgress000
flatten0.0010.0000.001
formulastring.to.list0.0010.0000.002
gatherCompound0.0010.0000.001
gatherData0.0000.0000.001
gatherDataBabel0.0010.0000.001
gatherDataUnknown0.0000.0000.001
gatherPubChem0.0010.0000.000
getCSID0.0010.0000.001
getCactus0.2830.0162.134
getCtsKey0.0050.0021.798
getCtsRecord0.0480.0020.393
getMolecule0.0730.0020.053
getPcId0.0120.0021.245
is.valid.formula0.0010.0010.002
loadInfolists0.0010.0000.001
loadList0.0010.0000.001
makeMollist0.0010.0000.001
makeRecalibration0.0010.0000.001
mbWorkflow0.0000.0000.001
order.formula0.0140.0000.014
parseMassBank0.0000.0000.001
plotMbWorkspaces0.0010.0000.000
ppm000
problematicPeaks000
reanalyzeFailpeaks0.0010.0000.001
recalibrate0.0010.0000.001
recalibrate.addMS1data0.0010.0000.001
smiles2mass0.0000.0010.001
to.limits.rcdk0.0030.0000.003
toMassbank0.0010.0000.001
toRMB000
updateSettings000
validate0.0010.0000.000