BioC 3.1: CHECK report for RMassBank on zin2

Package: RMassBank

Version: 1.10.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings RMassBank_1.10.0.tar.gz

StartedAt: 2015-10-05 04:56:09 -0700 (Mon, 05 Oct 2015)

EndedAt: 2015-10-05 04:57:17 -0700 (Mon, 05 Oct 2015)

EllapsedTime: 67.9 seconds

RetCode: 0

Status:  OK

CheckDir: RMassBank.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings RMassBank_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/RMassBank.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.10.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
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 ‘RMassBank’ can be installed ... [6s/6s] 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
'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 ... [4s/6s] 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
  ‘/home/biocbuild/bbs-3.1-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	0.000
RmbDefaultSettings	0.008	0.000	0.018
add.formula	0.004	0.000	0.003
addMB	0	0	0
addPeaks	0	0	0
addPeaksManually	0.001	0.000	0.001
aggregateSpectra	0	0	0
analyzeMsMs	0.000	0.004	0.000
annotator.default	0.000	0.000	0.001
archiveResults	0.000	0.000	0.002
c.msmsWSspecs	0.001	0.000	0.001
cleanElnoise	0.001	0.000	0.000
combineMultiplicities	0	0	0
compileRecord	0.001	0.000	0.001
createMolfile	0.001	0.000	0.000
dbe	0.000	0.000	0.001
deprofile	0.001	0.000	0.001
exportMassbank	0	0	0
filterLowaccResults	0.000	0.004	0.000
filterMultiplicity	0.000	0.000	0.001
filterPeakSatellites	0.000	0.000	0.001
filterPeaksMultiplicity	0	0	0
findMass	0.892	0.004	0.623
findMsMsHR	0.001	0.000	0.001
findMsMsHRperxcms.direct	0	0	0
findMz	0.001	0.000	0.000
findMz.formula	0.021	0.000	0.022
findProgress	0.000	0.004	0.000
flatten	0.000	0.000	0.001
formulastring.to.list	0.001	0.000	0.001
gatherCompound	0.000	0.000	0.001
gatherData	0.001	0.000	0.000
gatherDataBabel	0.000	0.000	0.001
gatherPubChem	0	0	0
getCactus	0.026	0.024	0.787
getCtsKey	0.005	0.000	1.273
getCtsRecord	0.011	0.000	0.173
getMolecule	0.041	0.000	0.040
getPcId	0.000	0.004	0.886
is.valid.formula	0.000	0.000	0.001
loadInfolists	0	0	0
loadList	0	0	0
makeMollist	0.001	0.000	0.001
makeRecalibration	0.000	0.000	0.001
mbWorkflow	0.001	0.000	0.000
order.formula	0.001	0.000	0.002
parseMassBank	0.000	0.000	0.001
plotMbWorkspaces	0	0	0
ppm	0.001	0.000	0.000
problematicPeaks	0.001	0.000	0.001
reanalyzeFailpeaks	0.000	0.000	0.001
recalibrate	0.001	0.000	0.001
recalibrate.addMS1data	0	0	0
smiles2mass	0.001	0.000	0.000
to.limits.rcdk	0.001	0.000	0.002
toMassbank	0.001	0.000	0.001
toRMB	0.000	0.000	0.001
updateSettings	0	0	0
validate	0.001	0.000	0.000