BioC 2.14: CHECK report for RMassBank on zin2

Package: RMassBank

Version: 1.6.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings RMassBank_1.6.0.tar.gz

StartedAt: 2014-10-08 02:26:12 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 02:27:30 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 77.6 seconds

RetCode: 0

Status:  OK

CheckDir: RMassBank.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings RMassBank_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/RMassBank.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-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 ‘1.6.0’
* 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 ... [7s/7s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/5s] 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
  ‘/home/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	0	0
CTS.externalIdTypes	0.000	0.000	0.001
RmbDefaultSettings	0.008	0.000	0.017
add.formula	0.004	0.000	0.004
addMB	0	0	0
addPeaks	0	0	0
addPeaksManually	0.004	0.000	0.000
aggregateSpectra	0	0	0
analyzeMsMs	0.004	0.000	0.000
annotator.default	0.000	0.000	0.001
archiveResults	0.004	0.000	0.003
cleanElnoise	0.004	0.000	0.001
combineMultiplicities	0.000	0.000	0.001
compileRecord	0.000	0.000	0.001
createMolfile	0	0	0
dbe	0.000	0.000	0.001
deprofile	0	0	0
exportMassbank	0.000	0.000	0.001
filterLowaccResults	0.000	0.000	0.001
filterMultiplicity	0	0	0
filterPeakSatellites	0.004	0.000	0.000
filterPeaksMultiplicity	0.000	0.000	0.001
findMass	0.840	0.020	0.675
findMsMsHR	0.000	0.000	0.001
findMsMsHRperxcms.direct	0.000	0.000	0.001
findMz	0.000	0.000	0.001
findMz.formula	0.024	0.000	0.028
findProgress	0	0	0
flatten	0.004	0.000	0.001
formulastring.to.list	0.000	0.000	0.001
gatherCompound	0.004	0.000	0.001
gatherData	0.000	0.000	0.001
getCactus	0.020	0.004	0.680
getCtsKey	0.000	0.004	0.063
getCtsRecord	0.012	0.000	0.185
getMolecule	0.048	0.000	0.046
getPcId	0	0	0
is.valid.formula	0.000	0.004	0.002
loadInfolists	0	0	0
loadList	0.000	0.000	0.001
makeMollist	0.000	0.000	0.001
makeRecalibration	0	0	0
mbWorkflow	0	0	0
order.formula	0.004	0.000	0.002
parseMassBank	0	0	0
plotMbWorkspaces	0.000	0.000	0.001
ppm	0.000	0.000	0.001
problematicPeaks	0	0	0
reanalyzeFailpeaks	0	0	0
recalibrate	0.000	0.000	0.001
recalibrate.addMS1data	0	0	0
smiles2mass	0	0	0
to.limits.rcdk	0.004	0.000	0.002
toMassbank	0.000	0.000	0.001
toRMB	0	0	0
updateSettings	0.000	0.000	0.001
validate	0.004	0.000	0.000