BioC 3.2: CHECK report for RMassBank on oaxaca

Package: RMassBank

Version: 1.12.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RMassBank_1.12.1.tar.gz

StartedAt: 2016-04-23 03:53:09 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:54:59 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 109.5 seconds

RetCode: 0

Status:  OK

CheckDir: RMassBank.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RMassBank_1.12.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/RMassBank.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.12.1’
* 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 ... [9s/10s] 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
'library' or 'require' calls in package code:
  ‘CAMERA’ ‘RMassBankData’ ‘RUnit’ ‘gplots’ ‘ontoCAT’ ‘xcms’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getInstruments: no visible global function definition for
  ‘getOntology’
.getInstruments: no visible global function definition for
  ‘getAllTermChildrenById’
.getInstruments: no visible global function definition for ‘getLabel’
.isOboReadable: no visible global function definition for ‘getOntology’
.isOboReadable: no visible global function definition for
  ‘getOntologyAccession’
.unitTestRMB: no visible global function definition for
  ‘defineTestSuite’
.unitTestRMB: no visible global function definition for ‘runTestSuite’
.unitTestRMB: no visible global function definition for
  ‘printTextProtocol’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘xcmsRaw’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘msn2xcmsRaw’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘xcmsSet’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘peaks<-’
findMsMsHRperxcms.direct: no visible binding for global variable
  ‘findPeaks’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘xsAnnotate’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘groupFWHM’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘plotPsSpectrum’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘getpspectra’
msmsRead.RAW: no visible global function definition for ‘xcmsSet’
msmsRead.RAW: no visible global function definition for ‘peaks<-’
msmsRead.RAW: no visible binding for global variable ‘findPeaks’
msmsRead.RAW: no visible global function definition for ‘xsAnnotate’
msmsRead.RAW: no visible global function definition for ‘groupFWHM’
msmsRead.RAW: no visible global function definition for
  ‘plotPsSpectrum’
msmsRead.RAW: no visible global function definition for ‘getpspectra’
plotRecalibration.direct: no visible global function definition for
  ‘hist2d’
validate: no visible global function definition for ‘defineTestSuite’
validate: no visible global function definition for ‘runTestSuite’
validate: no visible global function definition for ‘printHTMLProtocol’
* 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 ... [7s/17s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
getCtsKey 0.525  0.005    6.36
* 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-3.2-bioc/meat/RMassBank.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
CTS.externalIdSubset	0	0	0
CTS.externalIdTypes	0.001	0.000	0.001
RmbDefaultSettings	0.006	0.001	0.006
add.formula	0.004	0.001	0.003
addMB	0.001	0.000	0.001
addPeaks	0.000	0.000	0.001
addPeaksManually	0.001	0.000	0.001
aggregateSpectra	0.001	0.000	0.001
analyzeMsMs	0.001	0.000	0.001
annotator.default	0.001	0.000	0.000
archiveResults	0.002	0.000	0.002
c.msmsWSspecs	0.000	0.000	0.001
cleanElnoise	0.001	0.001	0.000
combineMultiplicities	0.001	0.000	0.001
compileRecord	0.000	0.000	0.001
createMolfile	0.000	0.000	0.001
dbe	0.001	0.000	0.000
deprofile	0.001	0.000	0.001
exportMassbank	0.001	0.000	0.001
filterLowaccResults	0.001	0.000	0.001
filterMultiplicity	0.000	0.000	0.001
filterPeakSatellites	0	0	0
filterPeaksMultiplicity	0.000	0.000	0.001
findMass	0.766	0.036	0.681
findMsMsHR	0.001	0.000	0.001
findMsMsHRperxcms.direct	0.001	0.000	0.000
findMz	0	0	0
findMz.formula	0.030	0.001	0.025
findProgress	0.000	0.000	0.001
flatten	0.001	0.000	0.000
formulastring.to.list	0.001	0.000	0.001
gatherCompound	0.001	0.000	0.001
gatherData	0	0	0
gatherDataBabel	0.000	0.000	0.001
gatherPubChem	0	0	0
getCactus	1.279	0.013	4.441
getCtsKey	0.525	0.005	6.360
getCtsRecord	0.015	0.002	0.151
getMolecule	0.053	0.000	0.053
getPcId	0.076	0.002	0.944
is.valid.formula	0.002	0.000	0.001
loadInfolists	0.001	0.000	0.001
loadList	0.000	0.001	0.001
makeMollist	0	0	0
makeRecalibration	0.000	0.000	0.001
mbWorkflow	0.000	0.001	0.001
order.formula	0.001	0.000	0.002
parseMassBank	0.001	0.000	0.001
plotMbWorkspaces	0.001	0.000	0.001
ppm	0.000	0.001	0.001
problematicPeaks	0.000	0.000	0.001
reanalyzeFailpeaks	0	0	0
recalibrate	0.001	0.000	0.002
recalibrate.addMS1data	0.000	0.000	0.001
smiles2mass	0	0	0
to.limits.rcdk	0.002	0.000	0.002
toMassbank	0.001	0.000	0.001
toRMB	0.001	0.000	0.000
updateSettings	0	0	0
validate	0.001	0.000	0.001