BioC 2.13: CHECK report for RMassBank on zin1

Package: RMassBank

Version: 1.4.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings RMassBank_1.4.0.tar.gz

StartedAt: 2014-04-05 03:37:38 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:38:57 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 79.2 seconds

RetCode: 0

Status:  OK

CheckDir: RMassBank.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/RMassBank.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.4.0’
* 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 ... [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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] 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
  ‘/home/biocbuild/bbs-2.13-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	0.004	0.000	0.002
CTS.externalIdTypes	0.004	0.000	0.005
RmbDefaultSettings	0.004	0.004	0.009
add.formula	0.008	0.000	0.007
addMB	0.000	0.000	0.002
addPeaks	0.004	0.000	0.004
addPeaksManually	0.004	0.000	0.003
aggregateSpectra	0.004	0.000	0.003
analyzeMsMs	0.000	0.000	0.002
annotator.default	0.004	0.000	0.002
archiveResults	0.000	0.004	0.005
cleanElnoise	0.004	0.000	0.003
combineMultiplicities	0.000	0.004	0.004
compileRecord	0.000	0.004	0.003
createMolfile	0.004	0.000	0.003
dbe	0.000	0.000	0.003
deprofile	0.004	0.000	0.003
exportMassbank	0.000	0.004	0.003
filterLowaccResults	0.000	0.000	0.003
filterMultiplicity	0.004	0.000	0.004
filterPeakSatellites	0.000	0.004	0.004
filterPeaksMultiplicity	0.004	0.000	0.003
findMass	1.904	0.036	1.158
findMsMsHR	0.008	0.000	0.003
findMz	0.008	0.000	0.003
findMz.formula	0.080	0.000	0.029
findProgress	0.008	0.000	0.003
flatten	0.008	0.000	0.003
formulastring.to.list	0.008	0.000	0.004
gatherCompound	0.004	0.000	0.003
gatherData	0.004	0.000	0.002
getCactus	0.044	0.000	0.605
getCtsKey	0.004	0.000	0.170
getCtsRecord	0.012	0.000	0.234
getMolecule	0.056	0.000	0.045
getPcId	0.004	0.004	0.503
is.valid.formula	0.004	0.000	0.003
loadInfolists	0.000	0.000	0.002
loadList	0.004	0.000	0.002
makeMollist	0.004	0.000	0.003
makeRecalibration	0.004	0.000	0.003
mbWorkflow	0.004	0.000	0.002
order.formula	0.008	0.000	0.004
parseMassBank	0.004	0.000	0.003
ppm	0.000	0.000	0.001
problematicPeaks	0.000	0.000	0.003
reanalyzeFailpeaks	0.004	0.000	0.003
recalibrate	0.004	0.000	0.006
recalibrate.addMS1data	0.000	0.000	0.002
smiles2mass	0.004	0.000	0.002
to.limits.rcdk	0.004	0.000	0.003
toMassbank	0.004	0.000	0.002
validate	0.004	0.000	0.002