BioC 3.1: CHECK report for RMassBank on petty

Package: RMassBank

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RMassBank_1.10.0.tar.gz

StartedAt: 2015-10-05 01:33:22 -0700 (Mon, 05 Oct 2015)

EndedAt: 2015-10-05 01:35:36 -0700 (Mon, 05 Oct 2015)

EllapsedTime: 134.6 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_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/RMassBank.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.10.0’
* 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 ... [13s/12s] 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’ ‘gplots’ ‘ontoCAT’ ‘RMassBankData’ ‘RUnit’ ‘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/9s] 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-3.1-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	0.000	0.000	0.001
CTS.externalIdTypes	0.001	0.000	0.002
RmbDefaultSettings	0.011	0.002	0.012
add.formula	0.006	0.000	0.006
addMB	0.001	0.000	0.001
addPeaks	0.001	0.000	0.001
addPeaksManually	0.000	0.001	0.000
aggregateSpectra	0.001	0.000	0.001
analyzeMsMs	0.000	0.000	0.001
annotator.default	0.000	0.000	0.001
archiveResults	0.003	0.001	0.004
c.msmsWSspecs	0.001	0.000	0.001
cleanElnoise	0.001	0.001	0.001
combineMultiplicities	0.001	0.000	0.002
compileRecord	0.001	0.000	0.001
createMolfile	0.001	0.000	0.001
dbe	0.002	0.000	0.002
deprofile	0.001	0.000	0.001
exportMassbank	0.001	0.000	0.001
filterLowaccResults	0.001	0.000	0.001
filterMultiplicity	0.001	0.000	0.002
filterPeakSatellites	0.001	0.000	0.000
filterPeaksMultiplicity	0.001	0.000	0.001
findMass	1.064	0.069	0.789
findMsMsHR	0.002	0.000	0.002
findMsMsHRperxcms.direct	0.001	0.000	0.002
findMz	0.001	0.000	0.001
findMz.formula	0.061	0.002	0.054
findProgress	0.001	0.000	0.001
flatten	0.002	0.000	0.002
formulastring.to.list	0.003	0.000	0.004
gatherCompound	0.001	0.001	0.001
gatherData	0.001	0.000	0.001
gatherDataBabel	0.001	0.000	0.001
gatherPubChem	0.001	0.000	0.001
getCactus	0.090	0.031	0.790
getCtsKey	0.008	0.001	1.456
getCtsRecord	0.022	0.003	0.194
getMolecule	0.085	0.002	0.087
getPcId	0.006	0.001	0.763
is.valid.formula	0.003	0.000	0.003
loadInfolists	0.001	0.001	0.002
loadList	0	0	0
makeMollist	0.001	0.000	0.001
makeRecalibration	0.001	0.000	0.001
mbWorkflow	0.001	0.000	0.001
order.formula	0.003	0.000	0.004
parseMassBank	0.001	0.000	0.002
plotMbWorkspaces	0.001	0.000	0.001
ppm	0.001	0.000	0.001
problematicPeaks	0.001	0.000	0.001
reanalyzeFailpeaks	0.001	0.000	0.002
recalibrate	0.003	0.000	0.003
recalibrate.addMS1data	0.002	0.000	0.002
smiles2mass	0.000	0.000	0.001
to.limits.rcdk	0.003	0.001	0.003
toMassbank	0.002	0.000	0.002
toRMB	0.001	0.000	0.001
updateSettings	0.001	0.000	0.001
validate	0.001	0.000	0.001