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BioC 3.5: CHECK report for RMassBank on tokay2

This page was generated on 2017-08-16 13:21:48 -0400 (Wed, 16 Aug 2017).

Package 1125/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RMassBank 2.4.0
RMassBank at Eawag
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/RMassBank
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RMassBank
Version: 2.4.0
Command: rm -rf RMassBank.buildbin-libdir RMassBank.Rcheck && mkdir RMassBank.buildbin-libdir RMassBank.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RMassBank.buildbin-libdir RMassBank_2.4.0.tar.gz >RMassBank.Rcheck\00install.out 2>&1 && cp RMassBank.Rcheck\00install.out RMassBank-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=RMassBank.buildbin-libdir --install="check:RMassBank-install.out" --force-multiarch --no-vignettes --timings RMassBank_2.4.0.tar.gz
StartedAt: 2017-08-16 02:31:16 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:35:15 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 238.5 seconds
RetCode: 0
Status:  OK  
CheckDir: RMassBank.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RMassBank.buildbin-libdir RMassBank.Rcheck && mkdir RMassBank.buildbin-libdir RMassBank.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RMassBank.buildbin-libdir RMassBank_2.4.0.tar.gz >RMassBank.Rcheck\00install.out 2>&1 && cp RMassBank.Rcheck\00install.out RMassBank-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=RMassBank.buildbin-libdir --install="check:RMassBank-install.out" --force-multiarch --no-vignettes --timings RMassBank_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/RMassBank.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RMassBank/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RMassBank' version '2.4.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'RMassBank' can be installed ... 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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 ... NOTE
.findPattern: no visible global function definition for
  'capture.output'
.get.mol2formula: no visible global function definition for
  'capture.output'
.pubChemOnline: no visible global function definition for 'URLencode'
addPeaks: no visible global function definition for 'read.csv'
analyzeMsMs.formula.optimized: no visible binding for global variable
  'occurrenceMatrix'
checkIsotopes: no visible global function definition for 'data'
checkIsotopes : <anonymous> : <anonymous>: no visible global function
  definition for 'points'
createSpecsFromPeaklists: no visible global function definition for
  'read.csv'
deprofile.spline : <anonymous>: no visible global function definition
  for 'smooth.spline'
deprofile.spline : <anonymous>: no visible global function definition
  for 'predict'
findEIC: no visible global function definition for 'predict'
findMsMsHRperxcms.direct : getRT : <anonymous>: no visible global
  function definition for 'median'
findMsMsHRperxcms.direct: no visible global function definition for
  'capture.output'
gatherSpectrum: no visible global function definition for
  'packageVersion'
getCSID: no visible global function definition for 'URLencode'
getCactus: no visible global function definition for 'URLencode'
getCtsKey: no visible global function definition for 'URLencode'
getMolecule: no visible global function definition for 'capture.output'
getPcCHEBI: no visible global function definition for 'URLencode'
getPcIUPAC: no visible global function definition for 'URLencode'
getPcId: no visible global function definition for 'URLencode'
getPcInchiKey: no visible global function definition for 'URLencode'
getPcSDF: no visible global function definition for 'URLencode'
getPcSynonym: no visible global function definition for 'URLencode'
loadInfolist: no visible global function definition for 'read.csv'
loadInfolist: no visible global function definition for 'read.csv2'
loadList: no visible global function definition for 'read.csv'
loadList: no visible global function definition for 'read.csv2'
makeMollist: no visible global function definition for 'write.table'
makeRecalibration: no visible global function definition for 'par'
mbWorkflow: no visible global function definition for 'write.csv'
msmsRead: no visible global function definition for 'read.csv'
msmsRead.RAW : getRT : <anonymous>: no visible global function
  definition for 'median'
msmsRead.RAW: no visible global function definition for
  'capture.output'
msmsRead.ticms2: no visible global function definition for 'read.csv'
msmsRead.ticms2: no visible global function definition for
  'c.msmsWSspecs'
newStep2WorkFlow: no visible global function definition for 'read.csv'
parseMassBank: no visible binding for global variable 'type.convert'
parseMassBank: no visible global function definition for
  'flush.console'
plotMbWorkspaces: no visible global function definition for 'points'
plotRecalibration: no visible global function definition for 'par'
plotRecalibration.direct: no visible global function definition for
  'predict'
plotRecalibration.direct: no visible global function definition for
  'lines'
plotRecalibration.direct: no visible global function definition for
  'heat.colors'
processProblematicPeaks: no visible global function definition for
  'write.csv'
progressBarHook: no visible global function definition for
  'txtProgressBar'
progressBarHook: no visible global function definition for
  'setTxtProgressBar'
recalibrate.identity: no visible global function definition for 'lm'
recalibrate.linear: no visible global function definition for 'lm'
recalibrate.loess: no visible global function definition for 'loess'
recalibrate.mean: no visible global function definition for 'lm'
recalibrateSingleSpec: no visible global function definition for
  'predict'
toRMB : <anonymous>: no visible global function definition for 'median'
show,mbWorkspace: no visible global function definition for 'str'
Undefined global functions or variables:
  URLencode c.msmsWSspecs capture.output data flush.console heat.colors
  lines lm loess median occurrenceMatrix packageVersion par points
  predict read.csv read.csv2 setTxtProgressBar smooth.spline str
  txtProgressBar type.convert write.csv write.table
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "lines", "par", "points")
  importFrom("stats", "lm", "loess", "median", "predict",
             "smooth.spline")
  importFrom("utils", "URLencode", "capture.output", "data",
             "flush.console", "packageVersion", "read.csv", "read.csv2",
             "setTxtProgressBar", "str", "txtProgressBar",
             "type.convert", "write.csv", "write.table")
to your NAMESPACE file.
* 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R'
 OK
** running tests for arch 'x64' ...
  Running 'doRUnit.R'
 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/RMassBank.Rcheck/00check.log'
for details.


RMassBank.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'RMassBank' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RMassBank' as RMassBank_2.4.0.zip
* DONE (RMassBank)

RMassBank.Rcheck/examples_i386/RMassBank-Ex.timings:

nameusersystemelapsed
CTS.externalIdSubset000
CTS.externalIdTypes000
RmbDefaultSettings0.000.000.02
add.formula0.050.000.05
addMB000
addPeaks000
addPeaksManually000
aggregateSpectra000
analyzeMsMs000
annotator.default000
archiveResults0.000.020.01
cleanElnoise000
combineMultiplicities000
compileRecord0.010.000.02
createMolfile000
dbe000
deprofile000
exportMassbank000
filterLowaccResults000
filterMultiplicity000
filterPeakSatellites000
filterPeaksMultiplicity000
findMass0.610.030.47
findMsMsHR000
findMsMsHRperxcms000
findMz000
findMz.formula0.040.000.25
findProgress000
flatten000
formulastring.to.list000
gatherCompound000
gatherData000
gatherDataBabel000
gatherDataUnknown000
gatherPubChem000
getCSID000
getCactus1.280.132.49
getCtsKey0.020.010.29
getCtsRecord0.060.000.43
getMolecule0.050.000.05
getPcId0.060.001.72
is.valid.formula000
loadInfolists000
loadList000
makeMollist000
makeRecalibration000
mbWorkflow000
order.formula0.030.000.03
parseMassBank000
plotMbWorkspaces000
ppm000
problematicPeaks000
reanalyzeFailpeaks000
recalibrate000
recalibrate.addMS1data0.020.000.02
smiles2mass000
to.limits.rcdk000
toMassbank000
toRMB000
updateSettings0.010.000.01
validate000

RMassBank.Rcheck/examples_x64/RMassBank-Ex.timings:

nameusersystemelapsed
CTS.externalIdSubset000
CTS.externalIdTypes000
RmbDefaultSettings0.000.000.05
add.formula0.060.000.06
addMB000
addPeaks000
addPeaksManually000
aggregateSpectra000
analyzeMsMs000
annotator.default000
archiveResults0.010.000.01
cleanElnoise0.020.000.02
combineMultiplicities000
compileRecord000
createMolfile000
dbe000
deprofile000
exportMassbank000
filterLowaccResults000
filterMultiplicity000
filterPeakSatellites000
filterPeaksMultiplicity000
findMass1.320.250.68
findMsMsHR000
findMsMsHRperxcms000
findMz000
findMz.formula0.060.000.03
findProgress000
flatten0.010.020.01
formulastring.to.list000
gatherCompound000
gatherData000
gatherDataBabel000
gatherDataUnknown0.030.000.02
gatherPubChem000
getCSID000
getCactus1.410.202.53
getCtsKey0.00.00.2
getCtsRecord0.080.020.47
getMolecule0.050.010.06
getPcId0.050.001.36
is.valid.formula000
loadInfolists000
loadList000
makeMollist000
makeRecalibration000
mbWorkflow000
order.formula0.030.000.04
parseMassBank000
plotMbWorkspaces000
ppm000
problematicPeaks000
reanalyzeFailpeaks000
recalibrate0.020.000.01
recalibrate.addMS1data000
smiles2mass000
to.limits.rcdk000
toMassbank000
toRMB000
updateSettings000
validate000