BioC 2.14: CHECK report for RMassBank on morelia

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: 2014-10-08 01:14:21 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:16:12 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 110.3 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-darwin13.1.0 (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 ... [9s/9s] 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
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 ... [5s/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

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	0.000	0.000	0.001
RmbDefaultSettings	0.007	0.002	0.049
add.formula	0.004	0.001	0.005
addMB	0.001	0.000	0.001
addPeaks	0.001	0.000	0.000
addPeaksManually	0.001	0.001	0.000
aggregateSpectra	0.000	0.000	0.001
analyzeMsMs	0	0	0
annotator.default	0.000	0.000	0.001
archiveResults	0.002	0.000	0.020
cleanElnoise	0.000	0.000	0.001
combineMultiplicities	0.000	0.000	0.001
compileRecord	0.000	0.000	0.001
createMolfile	0.000	0.000	0.001
dbe	0.001	0.000	0.002
deprofile	0.001	0.000	0.001
exportMassbank	0.001	0.000	0.001
filterLowaccResults	0.000	0.000	0.001
filterMultiplicity	0.000	0.000	0.001
filterPeakSatellites	0.000	0.000	0.001
filterPeaksMultiplicity	0	0	0
findMass	0.795	0.031	0.665
findMsMsHR	0.001	0.000	0.001
findMsMsHRperxcms.direct	0.001	0.000	0.001
findMz	0.001	0.000	0.001
findMz.formula	0.035	0.001	0.032
findProgress	0.001	0.000	0.000
flatten	0.001	0.000	0.000
formulastring.to.list	0.001	0.000	0.002
gatherCompound	0.000	0.000	0.001
gatherData	0	0	0
getCactus	0.113	0.002	0.579
getCtsKey	0.051	0.001	0.118
getCtsRecord	0.015	0.002	0.907
getMolecule	0.062	0.001	0.063
getPcId	0	0	0
is.valid.formula	0.001	0.001	0.001
loadInfolists	0.001	0.000	0.001
loadList	0.001	0.000	0.001
makeMollist	0.001	0.001	0.001
makeRecalibration	0.001	0.000	0.001
mbWorkflow	0.001	0.000	0.001
order.formula	0.002	0.000	0.003
parseMassBank	0.001	0.000	0.001
plotMbWorkspaces	0.001	0.000	0.001
ppm	0	0	0
problematicPeaks	0.000	0.000	0.001
reanalyzeFailpeaks	0.000	0.000	0.001
recalibrate	0.001	0.000	0.002
recalibrate.addMS1data	0.001	0.000	0.001
smiles2mass	0.001	0.000	0.000
to.limits.rcdk	0.002	0.000	0.002
toMassbank	0.001	0.000	0.001
toRMB	0.001	0.000	0.001
updateSettings	0.001	0.000	0.001
validate	0.000	0.000	0.001