BioC 2.12: CHECK report for RMassBank on george2

Package: RMassBank

Version: 1.2.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RMassBank_1.2.1.tar.gz

StartedAt: 2013-10-09 04:39:03 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:41:43 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 160.4 seconds

RetCode: 0

Status:  OK

CheckDir: RMassBank.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/RMassBank.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.2.1’
* 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 ... [12s/13s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* 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 examples ... [10s/12s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-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	0.008	0.000	0.008
CTS.externalIdTypes	0.016	0.004	0.018
RmbDefaultSettings	0.020	0.008	0.025
add.formula	0.020	0.000	0.019
addPeaks	0.008	0.000	0.007
aggregateSpectra	0.008	0.000	0.010
analyzeMsMs	0.008	0.000	0.007
archiveResults	0.020	0.000	0.019
cleanElnoise	0.004	0.004	0.008
compileRecord	0.000	0.008	0.011
createMolfile	0.008	0.000	0.009
dbe	0.208	0.012	0.220
deprofile	0.008	0.008	0.017
exportMassbank	0.004	0.004	0.009
filterLowaccResults	0.000	0.008	0.007
filterMultiplicity	0.008	0.004	0.012
filterPeakSatellites	0.012	0.008	0.019
filterPeaksMultiplicity	0.008	0.000	0.009
findMass	1.988	0.108	1.562
findMsMsHR	0.032	0.004	0.016
findMz	0.028	0.000	0.013
findMz.formula	0.104	0.000	0.044
flatten	0.024	0.004	0.013
formulastring.to.list	0.032	0.004	0.014
gatherCompound	0.016	0.008	0.012
gatherData	0.004	0.004	0.005
getCactus	0.040	0.004	0.679
getCtsKey	0.012	0.004	0.118
getCtsRecord	0.020	0.012	2.393
getMolecule	0.084	0.004	0.089
getPcId	0.024	0.000	0.349
is.valid.formula	0.020	0.000	0.018
loadInfolists	0.016	0.000	0.018
loadList	0.008	0.000	0.009
makeMollist	0.012	0.004	0.016
makeRecalibration	0.020	0.000	0.019
mbWorkflow	0.016	0.000	0.017
order.formula	0.020	0.000	0.019
ppm	0.012	0.000	0.015
problematicPeaks	0.016	0.000	0.017
reanalyzeFailpeaks	0.016	0.000	0.014
recalibrate	0.028	0.000	0.025
recalibrate.addMS1data	0.016	0.000	0.014
to.limits.rcdk	0.012	0.000	0.013
toMassbank	0.016	0.000	0.016