BioC 2.13: CHECK report for RMassBank on perceval

Package: RMassBank

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RMassBank_1.4.0.tar.gz

StartedAt: 2014-04-05 03:58:36 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:00:56 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 140.2 seconds

RetCode: 0

Status:  OK

CheckDir: RMassBank.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/RMassBank.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.4.0’
* 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 ... [13s/13s] 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... [9s/10s] 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/RMassBank.Rcheck/00check.log’
for details.

* installing *source* package ‘RMassBank’ ...
** R
** inst
** preparing package for lazy loading
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.11.0)
than is installed on your system (0.11.1). This might lead to errors
when loading mzR. If you encounter such issues, please send
a report, including the output of sessionInfo() to the Bioc
mailing list -- http://www.bioconductor.org/help/mailing-list.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.11.0)
than is installed on your system (0.11.1). This might lead to errors
when loading mzR. If you encounter such issues, please send
a report, including the output of sessionInfo() to the Bioc
mailing list -- http://www.bioconductor.org/help/mailing-list.
* DONE (RMassBank)

name	user	system	elapsed
CTS.externalIdSubset	0.008	0.001	0.009
CTS.externalIdTypes	0.017	0.001	0.019
RmbDefaultSettings	0.017	0.004	0.021
add.formula	0.019	0.002	0.025
addMB	0.009	0.001	0.089
addPeaks	0.006	0.001	0.006
addPeaksManually	0.006	0.001	0.007
aggregateSpectra	0.007	0.001	0.007
analyzeMsMs	0.007	0.001	0.007
annotator.default	0.009	0.001	0.012
archiveResults	0.010	0.001	0.012
cleanElnoise	0.006	0.002	0.008
combineMultiplicities	0.008	0.002	0.008
compileRecord	0.004	0.000	0.005
createMolfile	0.004	0.000	0.004
dbe	0.007	0.001	0.008
deprofile	0.008	0.001	0.009
exportMassbank	0.007	0.001	0.009
filterLowaccResults	0.005	0.001	0.006
filterMultiplicity	0.006	0.001	0.007
filterPeakSatellites	0.007	0.001	0.009
filterPeaksMultiplicity	0.008	0.001	0.009
findMass	2.084	0.137	1.595
findMsMsHR	0.018	0.001	0.006
findMz	0.018	0.001	0.006
findMz.formula	0.044	0.002	0.040
findProgress	0.006	0.001	0.006
flatten	0.007	0.001	0.007
formulastring.to.list	0.011	0.002	0.013
gatherCompound	0.010	0.000	0.011
gatherData	0.006	0.001	0.005
getCactus	0.033	0.004	0.980
getCtsKey	0.018	0.003	0.104
getCtsRecord	0.021	0.003	0.253
getMolecule	0.097	0.002	0.084
getPcId	0.014	0.001	0.236
is.valid.formula	0.009	0.001	0.009
loadInfolists	0.005	0.000	0.006
loadList	0.006	0.000	0.007
makeMollist	0.200	0.001	0.201
makeRecalibration	0.007	0.000	0.008
mbWorkflow	0.005	0.002	0.006
order.formula	0.008	0.001	0.009
parseMassBank	0.004	0.001	0.005
ppm	0.004	0.000	0.005
problematicPeaks	0.007	0.000	0.008
reanalyzeFailpeaks	0.005	0.000	0.005
recalibrate	0.015	0.001	0.017
recalibrate.addMS1data	0.008	0.000	0.009
smiles2mass	0.007	0.001	0.007
to.limits.rcdk	0.011	0.001	0.013
toMassbank	0.008	0.001	0.009
validate	0.009	0.000	0.010