BioC 2.14: CHECK report for RMassBank on petty

Package: RMassBank

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RMassBank_1.6.0.tar.gz

StartedAt: 2014-10-06 23:50:23 -0700 (Mon, 06 Oct 2014)

EndedAt: 2014-10-06 23:53:33 -0700 (Mon, 06 Oct 2014)

EllapsedTime: 189.7 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 --no-multiarch RMassBank_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/RMassBank.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.6.0’
* 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 ... [16s/17s] 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
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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... [9s/10s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.001	0.000	0.001
CTS.externalIdTypes	0.001	0.000	0.002
RmbDefaultSettings	0.010	0.003	0.014
add.formula	0.007	0.001	0.008
addMB	0.000	0.000	0.001
addPeaks	0.000	0.000	0.001
addPeaksManually	0.001	0.000	0.002
aggregateSpectra	0.002	0.000	0.002
analyzeMsMs	0.002	0.000	0.001
annotator.default	0.001	0.000	0.001
archiveResults	0.006	0.001	0.007
cleanElnoise	0.001	0.000	0.001
combineMultiplicities	0.002	0.000	0.002
compileRecord	0.002	0.000	0.002
createMolfile	0.002	0.000	0.001
dbe	0.002	0.000	0.003
deprofile	0.001	0.000	0.001
exportMassbank	0.001	0.001	0.001
filterLowaccResults	0.000	0.000	0.001
filterMultiplicity	0.001	0.001	0.001
filterPeakSatellites	0.002	0.000	0.002
filterPeaksMultiplicity	0.001	0.001	0.002
findMass	1.222	0.079	0.981
findMsMsHR	0.001	0.000	0.002
findMsMsHRperxcms.direct	0.001	0.000	0.001
findMz	0.001	0.000	0.001
findMz.formula	0.075	0.002	0.069
findProgress	0.001	0.000	0.001
flatten	0.001	0.000	0.001
formulastring.to.list	0.004	0.000	0.004
gatherCompound	0.001	0.000	0.001
gatherData	0.001	0.000	0.000
getCactus	0.040	0.003	0.558
getCtsKey	0.008	0.002	0.493
getCtsRecord	0.150	0.002	0.492
getMolecule	0.103	0.001	0.107
getPcId	0.001	0.000	0.001
is.valid.formula	0.003	0.001	0.003
loadInfolists	0.001	0.000	0.002
loadList	0.001	0.000	0.001
makeMollist	0.002	0.000	0.002
makeRecalibration	0.002	0.000	0.002
mbWorkflow	0.001	0.000	0.001
order.formula	0.004	0.000	0.004
parseMassBank	0.001	0.001	0.001
plotMbWorkspaces	0.001	0.000	0.001
ppm	0.001	0.001	0.001
problematicPeaks	0.001	0.000	0.002
reanalyzeFailpeaks	0.001	0.000	0.002
recalibrate	0.002	0.000	0.003
recalibrate.addMS1data	0.002	0.000	0.002
smiles2mass	0.001	0.001	0.002
to.limits.rcdk	0.004	0.001	0.004
toMassbank	0.001	0.001	0.001
toRMB	0.001	0.000	0.001
updateSettings	0.001	0.000	0.002
validate	0.001	0.001	0.001