Package: RMassBank

Version: 1.1.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RMassBank_1.1.0.tar.gz

StartedAt: 2013-01-16 05:58:19 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 06:00:02 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 102.4 seconds

RetCode: 0

Status:  OK

CheckDir: RMassBank.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/RMassBank.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.1.0’
* 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 ... 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 ... 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
  ‘/loc/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
   ‘RMassBank.Rnw’ 
** testing if installed package can be loaded

* DONE (RMassBank)

name	user	system	elapsed
RmbDefaultSettings	0.008	0.004	0.014
add.formula	0.016	0.000	0.015
addPeaks	0.004	0.000	0.005
aggregateSpectra	0.008	0.000	0.008
analyzeMsMs	0.004	0.000	0.006
archiveResults	0.008	0.000	0.008
cleanElnoise	0.144	0.000	0.146
compileRecord	0.008	0.000	0.009
createMolfile	0.012	0.000	0.012
dbe	0.012	0.000	0.011
deprofile	0.008	0.000	0.009
exportMassbank	0.008	0.000	0.009
filterLowaccResults	0.008	0.000	0.007
filterMultiplicity	0.004	0.000	0.007
filterPeakSatellites	0.008	0.000	0.011
filterPeaksMultiplicity	0.008	0.000	0.007
findMass	1.652	0.064	1.260
findMsMsHR	0.052	0.000	0.029
findMz	0.008	0.000	0.006
findMz.formula	0.028	0.004	0.055
flatten	0.008	0.004	0.014
formulastring.to.list	0.012	0.000	0.011
gatherCompound	0.024	0.000	0.023
gatherData	0.14	0.00	0.14
getCactus	0.036	0.000	0.595
getCtsRecord	0.024	0.000	0.132
getMolecule	0.108	0.000	0.101
getPcId	0.012	0.000	0.252
is.valid.formula	0.012	0.000	0.011
loadInfolists	0.004	0.000	0.007
loadList	0.004	0.000	0.004
makeMollist	0.008	0.000	0.008
makeRecalibration	0.012	0.000	0.010
mbWorkflow	0.004	0.004	0.007
order.formula	0.008	0.000	0.009
ppm	0.004	0.000	0.005
problematicPeaks	0.008	0.000	0.008
reanalyzeFailpeaks	0.008	0.000	0.008
recalibrate	0.012	0.000	0.015
recalibrate.addMS1data	0.004	0.000	0.007
to.limits.rcdk	0.008	0.000	0.009
toMassbank	0.012	0.000	0.010