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BioC 2.14: CHECK report for RMassBank on petty

This page was generated on 2014-10-07 08:57:16 -0700 (Tue, 07 Oct 2014).

Package 669/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RMassBank 1.6.0
RMassBank at Eawag
Snapshot Date: 2014-10-06 17:20:37 -0700 (Mon, 06 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/RMassBank
Last Changed Rev: 88838 / Revision: 95036
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: RMassBank
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RMassBank_1.6.0.tar.gz
StartedAt: 2014-10-06 23:50:23 -0700 (Mon, 06 Oct 2014)
EndedAt: 2014-10-06 23:53:33 -0700 (Mon, 06 Oct 2014)
EllapsedTime: 189.7 seconds
RetCode: 0
Status:  OK 
CheckDir: RMassBank.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RMassBank_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/RMassBank.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.6.0’
* 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 ... [16s/17s] 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 ... NOTE
Package in Depends field not imported from: ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/RMassBank.Rcheck/00check.log’
for details.

RMassBank.Rcheck/00install.out:

* 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)

RMassBank.Rcheck/RMassBank-Ex.timings:

nameusersystemelapsed
CTS.externalIdSubset0.0010.0000.001
CTS.externalIdTypes0.0010.0000.002
RmbDefaultSettings0.0100.0030.014
add.formula0.0070.0010.008
addMB0.0000.0000.001
addPeaks0.0000.0000.001
addPeaksManually0.0010.0000.002
aggregateSpectra0.0020.0000.002
analyzeMsMs0.0020.0000.001
annotator.default0.0010.0000.001
archiveResults0.0060.0010.007
cleanElnoise0.0010.0000.001
combineMultiplicities0.0020.0000.002
compileRecord0.0020.0000.002
createMolfile0.0020.0000.001
dbe0.0020.0000.003
deprofile0.0010.0000.001
exportMassbank0.0010.0010.001
filterLowaccResults0.0000.0000.001
filterMultiplicity0.0010.0010.001
filterPeakSatellites0.0020.0000.002
filterPeaksMultiplicity0.0010.0010.002
findMass1.2220.0790.981
findMsMsHR0.0010.0000.002
findMsMsHRperxcms.direct0.0010.0000.001
findMz0.0010.0000.001
findMz.formula0.0750.0020.069
findProgress0.0010.0000.001
flatten0.0010.0000.001
formulastring.to.list0.0040.0000.004
gatherCompound0.0010.0000.001
gatherData0.0010.0000.000
getCactus0.0400.0030.558
getCtsKey0.0080.0020.493
getCtsRecord0.1500.0020.492
getMolecule0.1030.0010.107
getPcId0.0010.0000.001
is.valid.formula0.0030.0010.003
loadInfolists0.0010.0000.002
loadList0.0010.0000.001
makeMollist0.0020.0000.002
makeRecalibration0.0020.0000.002
mbWorkflow0.0010.0000.001
order.formula0.0040.0000.004
parseMassBank0.0010.0010.001
plotMbWorkspaces0.0010.0000.001
ppm0.0010.0010.001
problematicPeaks0.0010.0000.002
reanalyzeFailpeaks0.0010.0000.002
recalibrate0.0020.0000.003
recalibrate.addMS1data0.0020.0000.002
smiles2mass0.0010.0010.002
to.limits.rcdk0.0040.0010.004
toMassbank0.0010.0010.001
toRMB0.0010.0000.001
updateSettings0.0010.0000.002
validate0.0010.0010.001