BioC 2.12: CHECK report for RMassBank on petty

Package: RMassBank

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RMassBank_1.2.1.tar.gz

StartedAt: 2013-10-08 23:43:55 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:46:58 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 182.8 seconds

RetCode: 0

Status:  OK

CheckDir: RMassBank.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/RMassBank.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 ... [15s/21s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [11s/16s] 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
  '/Users/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	0.011	0.000	0.012
CTS.externalIdTypes	0.006	0.001	0.007
RmbDefaultSettings	0.015	0.003	0.018
add.formula	0.016	0.001	0.017
addPeaks	0.006	0.001	0.006
aggregateSpectra	0.009	0.001	0.010
analyzeMsMs	0.007	0.001	0.007
archiveResults	0.010	0.001	0.012
cleanElnoise	0.010	0.001	0.011
compileRecord	0.139	0.002	0.142
createMolfile	0.006	0.001	0.008
dbe	0.005	0.001	0.005
deprofile	0.008	0.001	0.009
exportMassbank	0.007	0.001	0.009
filterLowaccResults	0.006	0.001	0.007
filterMultiplicity	0.007	0.001	0.009
filterPeakSatellites	0.008	0.001	0.009
filterPeaksMultiplicity	0.007	0.001	0.008
findMass	3.198	0.161	1.894
findMsMsHR	0.030	0.001	0.011
findMz	0.023	0.001	0.008
findMz.formula	0.142	0.003	0.061
flatten	0.010	0.001	0.011
formulastring.to.list	0.010	0.001	0.010
gatherCompound	0.016	0.001	0.019
gatherData	0.004	0.001	0.004
getCactus	0.045	0.005	2.986
getCtsKey	0.010	0.001	0.181
getCtsRecord	0.023	0.004	2.492
getMolecule	0.105	0.002	0.084
getPcId	0.146	0.001	0.408
is.valid.formula	0.014	0.001	0.015
loadInfolists	0.016	0.000	0.017
loadList	0.004	0.001	0.005
makeMollist	0.007	0.000	0.007
makeRecalibration	0.007	0.000	0.007
mbWorkflow	0.011	0.001	0.012
order.formula	0.010	0.001	0.010
ppm	0.013	0.000	0.022
problematicPeaks	0.008	0.001	0.018
reanalyzeFailpeaks	0.006	0.001	0.007
recalibrate	0.016	0.001	0.027
recalibrate.addMS1data	0.009	0.001	0.013
to.limits.rcdk	0.011	0.001	0.020
toMassbank	0.011	0.001	0.013