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BioC 3.1: CHECK report for RMassBank on zin2

This page was generated on 2015-10-05 09:24:17 -0700 (Mon, 05 Oct 2015).

Package 828/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RMassBank 1.10.0
RMassBank at Eawag
Snapshot Date: 2015-10-04 17:20:20 -0700 (Sun, 04 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/RMassBank
Last Changed Rev: 102591 / Revision: 109170
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RMassBank
Version: 1.10.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings RMassBank_1.10.0.tar.gz
StartedAt: 2015-10-05 04:56:09 -0700 (Mon, 05 Oct 2015)
EndedAt: 2015-10-05 04:57:17 -0700 (Mon, 05 Oct 2015)
EllapsedTime: 67.9 seconds
RetCode: 0
Status:  OK 
CheckDir: RMassBank.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings RMassBank_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/RMassBank.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.10.0’
* package encoding: UTF-8
* 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 ... [6s/6s] 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
'library' or 'require' calls in package code:
  ‘CAMERA’ ‘RMassBankData’ ‘RUnit’ ‘gplots’ ‘ontoCAT’ ‘xcms’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getInstruments: no visible global function definition for
  ‘getOntology’
.getInstruments: no visible global function definition for
  ‘getAllTermChildrenById’
.getInstruments: no visible global function definition for ‘getLabel’
.isOboReadable: no visible global function definition for ‘getOntology’
.isOboReadable: no visible global function definition for
  ‘getOntologyAccession’
.unitTestRMB: no visible global function definition for
  ‘defineTestSuite’
.unitTestRMB: no visible global function definition for ‘runTestSuite’
.unitTestRMB: no visible global function definition for
  ‘printTextProtocol’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘xcmsRaw’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘msn2xcmsRaw’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘xcmsSet’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘peaks<-’
findMsMsHRperxcms.direct: no visible binding for global variable
  ‘findPeaks’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘xsAnnotate’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘groupFWHM’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘plotPsSpectrum’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘getpspectra’
msmsRead.RAW: no visible global function definition for ‘xcmsSet’
msmsRead.RAW: no visible global function definition for ‘peaks<-’
msmsRead.RAW: no visible binding for global variable ‘findPeaks’
msmsRead.RAW: no visible global function definition for ‘xsAnnotate’
msmsRead.RAW: no visible global function definition for ‘groupFWHM’
msmsRead.RAW: no visible global function definition for
  ‘plotPsSpectrum’
msmsRead.RAW: no visible global function definition for ‘getpspectra’
plotRecalibration.direct: no visible global function definition for
  ‘hist2d’
validate: no visible global function definition for ‘defineTestSuite’
validate: no visible global function definition for ‘runTestSuite’
validate: no visible global function definition for ‘printHTMLProtocol’
* 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 ... [4s/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
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-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.externalIdSubset000
CTS.externalIdTypes0.0010.0000.000
RmbDefaultSettings0.0080.0000.018
add.formula0.0040.0000.003
addMB000
addPeaks000
addPeaksManually0.0010.0000.001
aggregateSpectra000
analyzeMsMs0.0000.0040.000
annotator.default0.0000.0000.001
archiveResults0.0000.0000.002
c.msmsWSspecs0.0010.0000.001
cleanElnoise0.0010.0000.000
combineMultiplicities000
compileRecord0.0010.0000.001
createMolfile0.0010.0000.000
dbe0.0000.0000.001
deprofile0.0010.0000.001
exportMassbank000
filterLowaccResults0.0000.0040.000
filterMultiplicity0.0000.0000.001
filterPeakSatellites0.0000.0000.001
filterPeaksMultiplicity000
findMass0.8920.0040.623
findMsMsHR0.0010.0000.001
findMsMsHRperxcms.direct000
findMz0.0010.0000.000
findMz.formula0.0210.0000.022
findProgress0.0000.0040.000
flatten0.0000.0000.001
formulastring.to.list0.0010.0000.001
gatherCompound0.0000.0000.001
gatherData0.0010.0000.000
gatherDataBabel0.0000.0000.001
gatherPubChem000
getCactus0.0260.0240.787
getCtsKey0.0050.0001.273
getCtsRecord0.0110.0000.173
getMolecule0.0410.0000.040
getPcId0.0000.0040.886
is.valid.formula0.0000.0000.001
loadInfolists000
loadList000
makeMollist0.0010.0000.001
makeRecalibration0.0000.0000.001
mbWorkflow0.0010.0000.000
order.formula0.0010.0000.002
parseMassBank0.0000.0000.001
plotMbWorkspaces000
ppm0.0010.0000.000
problematicPeaks0.0010.0000.001
reanalyzeFailpeaks0.0000.0000.001
recalibrate0.0010.0000.001
recalibrate.addMS1data000
smiles2mass0.0010.0000.000
to.limits.rcdk0.0010.0000.002
toMassbank0.0010.0000.001
toRMB0.0000.0000.001
updateSettings000
validate0.0010.0000.000