##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:RMassBank.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RMassBank_3.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/RMassBank.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '3.2.0'
* 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
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'RMassBank' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/meat/RMassBank/man/dot-parseTitleString.Rd:38: missing link 'compileRecord'
  Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/meat/RMassBank/man/exportMassbank.Rd:11: missing link 'compileRecord'
  Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/meat/RMassBank/man/exportMassbank.Rd:52: missing link 'compileRecord'
  Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/meat/RMassBank/man/getAnalyticalInfo.Rd:71: missing link 'compileRecord'
  Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/meat/RMassBank/man/toMassbank.Rd:79: missing link 'compileRecord'
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/RMassBank.Rcheck/00install.out' for details.
* 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
Unexported object imported by a ':::' call: 'MSnbase:::writeMgfContent'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.precursorTypes'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... WARNING
  'property<-'
  '\S4method{property<-}{RmbSpectrum2,character,ANY,logical,character}'
  '\S4method{property<-}{RmbSpectrum2,character,ANY,logical,missing}'
  '\S4method{property<-}{RmbSpectrum2,character,ANY,missing,character}'
  '\S4method{property<-}{RmbSpectrum2,character,ANY,missing,missing}'
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.buildRecord.RmbSpectrum2: no visible global function definition for
  'packageVersion'
.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'
.selfDefinedAccessionBuilder: no visible binding for global variable
  'accessionBuilder'
.selfDefinedAccessionBuilder: no visible global function definition for
  'accessionBuilder'
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: no visible binding for global variable 'msmsPeaks'
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'
gatherDataMinimal.spectrum: no visible binding for global variable
  'cpd'
getCSID: no visible global function definition for 'URLencode'
getCactus: no visible global function definition for 'URLencode'
getCompTox: no visible global function definition for 'URLencode'
getCtsKey: no visible global function definition for 'URLencode'
getCtsRecord: no visible global function definition for 'URLencode'
getMolecule: no visible global function definition for 'capture.output'
getMonoisotopicMass: no visible global function definition for 'data'
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'
mbWorkflow : <anonymous>: no visible binding for global variable
  'filterOK'
mbWorkflow : <anonymous>: no visible binding for global variable 'best'
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'
parseMbRecord: no visible binding for global variable 'type.convert'
parseMbRecord: 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'
reanalyzeFailpeak: no visible binding for global variable 'mass.calc'
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'
retrieveDataWithRetry: no visible global function definition for
  'URLencode'
toRMB : <anonymous>: no visible global function definition for 'median'
show,mbWorkspace: no visible global function definition for 'str'
updateObject,RmbSpectraSet: no visible global function definition for
  'updateObjectFromSlots'
Undefined global functions or variables:
  URLencode accessionBuilder best c.msmsWSspecs capture.output cpd data
  filterOK flush.console heat.colors lines lm loess mass.calc median
  msmsPeaks occurrenceMatrix packageVersion par points predict read.csv
  read.csv2 setTxtProgressBar smooth.spline str txtProgressBar
  type.convert updateObjectFromSlots 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 ... NOTE
prepare_Rd: dot-updateObject.RmbSpectrum2.formulaSource.Rd:12-14: Dropping empty section \value
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'parseMassBank':
  'parseMassBank.Rd' 'parseMbRecord.Rd'
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'dot-parseTitleString.Rd':
  'compileRecord'

Missing link or links in documentation object 'exportMassbank.Rd':
  'compileRecord'

Missing link or links in documentation object 'getAnalyticalInfo.Rd':
  'compileRecord'

Missing link or links in documentation object 'toMassbank.Rd':
  'compileRecord'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'buildRecord' 'findMsMsHRperMsp.direct' 'mergePeaks' 'mergeSpectra'
  'mergeSpectra.RmbSpectrum2List' 'property' 'property<-'
Undocumented S4 classes:
  'RmbSpectrum2' 'RmbSpectraSetList' 'RmbSpectraSet' 'RmbSpectrum2List'
Undocumented S4 methods:
  generic '+' and siglist 'RmbSpectraSet,ANY'
  generic '+' and siglist 'RmbSpectrum2List,ANY'
  generic '+' and siglist 'Spectrum,numeric'
  generic '-' and siglist 'RmbSpectraSet,ANY'
  generic '-' and siglist 'RmbSpectrum2List,ANY'
  generic '-' and siglist 'Spectrum,numeric'
  generic 'buildRecord' and siglist 'RmbSpectraSet'
  generic 'buildRecord' and siglist 'RmbSpectrum2'
  generic 'cleanElnoise' and siglist 'RmbSpectraSet,numeric,numeric'
  generic 'cleanElnoise' and siglist 'RmbSpectrum2,numeric,numeric'
  generic 'cleanElnoise' and siglist 'data.frame,numeric,numeric'
  generic 'fillback' and siglist 'RmbSpectraSet'
  generic 'fillback' and siglist 'RmbSpectrum2'
  generic 'fillback' and siglist 'msmsWorkspace'
  generic 'mergePeaks' and siglist 'RmbSpectrum2'
  generic 'mergePeaks' and siglist 'Spectrum'
  generic 'mergePeaks' and siglist 'data.frame'
  generic 'mergePeaks' and siglist 'matrix'
  generic 'mergeSpectra' and siglist 'RmbSpectrum2List'
  generic 'normalize' and siglist 'RmbSpectrum2'
  generic 'normalize' and siglist 'RmbSpectrum2List'
  generic 'property' and siglist 'RmbSpectrum2,character'
  generic 'property<-' and siglist
    'RmbSpectrum2,character,ANY,logical,character'
  generic 'property<-' and siglist
    'RmbSpectrum2,character,ANY,logical,missing'
  generic 'property<-' and siglist
    'RmbSpectrum2,character,ANY,missing,character'
  generic 'property<-' and siglist
    'RmbSpectrum2,character,ANY,missing,missing'
  generic 'selectPeaks' and siglist 'RmbSpectraSet'
  generic 'selectPeaks' and siglist 'Spectrum'
  generic 'toMassbank' and siglist 'RmbSpectraSet'
  generic 'toMassbank' and siglist 'RmbSpectrum2'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object '.buildRecord.RmbSpectraSet' but not in code:
  'compileRecord'

Functions or methods with usage in documentation object 'getAnalyticalInfo' but not in code:
  'gatherCompound' 'gatherSpectrum'

Codoc mismatches from documentation object 'exportMassbank':
exportMassbank
  Code: function(compiled, molfile = NULL)
  Docs: function(compiled, files, molfile)
  Argument names in docs not in code:
    files
  Mismatches in argument names:
    Position: 2 Code: molfile Docs: files
  Mismatches in argument default values:
    Name: 'molfile' Code: NULL Docs: 

Codoc mismatches from documentation object 'filterPeaksMultiplicity':
filterPeaksMultiplicity
  Code: function(w, recalcBest = TRUE)
  Docs: function(peaks, formulacol, recalcBest = TRUE)
  Argument names in code not in docs:
    w
  Argument names in docs not in code:
    peaks formulacol
  Mismatches in argument names:
    Position: 1 Code: w Docs: peaks
    Position: 2 Code: recalcBest Docs: formulacol

Codoc mismatches from documentation object 'findMz':
findMz
  Code: function(cpdID, mode = "pH", ppm = 10, deltaMz = 0, retrieval =
                 "standard", unknownMass =
                 getOption("RMassBank")$unknownMass)
  Docs: function(cpdID, mode = "pH", ppm = 10, deltaMz = 0, retrieval =
                 "standard")
  Argument names in code not in docs:
    unknownMass

Codoc mismatches from documentation object 'problematicPeaks':
problematicPeaks
  Code: function(sp)
  Docs: function(peaks_unmatched, peaks_matched, mode = "pH")
  Argument names in code not in docs:
    sp
  Argument names in docs not in code:
    peaks_unmatched peaks_matched mode
  Mismatches in argument names:
    Position: 1 Code: sp Docs: peaks_unmatched

Codoc mismatches from documentation object 'reanalyzeFailpeaks':
reanalyzeFailpeaks
  Code: function(w, custom_additions, mode, filterSettings =
                 getOption("RMassBank")$filterSettings, progressbar =
                 "progressBarHook")
  Docs: function(aggregated, custom_additions, mode, filterSettings =
                 getOption("RMassBank")$filterSettings, progressbar =
                 "progressBarHook")
  Argument names in code not in docs:
    w
  Argument names in docs not in code:
    aggregated
  Mismatches in argument names:
    Position: 1 Code: w Docs: aggregated
reanalyzeFailpeak
  Code: function(mass, custom_additions, cpdID, mode, filterSettings =
                 getOption("RMassBank")$filterSettings)
  Docs: function(custom_additions, mass, cpdID, counter, pb = NULL,
                 mode, filterSettings =
                 getOption("RMassBank")$filterSettings)
  Argument names in docs not in code:
    counter pb
  Mismatches in argument names (first 3):
    Position: 1 Code: mass Docs: custom_additions
    Position: 2 Code: custom_additions Docs: mass
    Position: 4 Code: mode Docs: counter

Codoc mismatches from documentation object 'toMassbank':
toMassbank
  Code: function(o, ...)
  Docs: function(mbdata)
  Argument names in code not in docs:
    o ...
  Argument names in docs not in code:
    mbdata
  Mismatches in argument names:
    Position: 1 Code: o Docs: mbdata

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'annotator.default'
  'formulaTag'
Documented arguments not in \usage in documentation object 'annotator.default':
  'type'

Objects in \usage without \alias in documentation object '.buildRecord.RmbSpectraSet':
  'compileRecord'

Undocumented arguments in documentation object 'fillback'
  'o' '...'

Undocumented arguments in documentation object 'findEIC'
  'polarity' 'msLevel' 'precursor'

Undocumented arguments in documentation object 'findMsMsHR'
  'enforcePolarity' 'polarity'

Undocumented arguments in documentation object 'mergePeaks.df'
  'peaks' 'dppm' 'dabs' 'int'

Documented arguments not in \usage in documentation object 'processProblematicPeaks':
  'mode'

Undocumented arguments in documentation object 'selectPeaks'
  'filter' 'enclos' 'peaks' 'noise' 'width'
Documented arguments not in \usage in documentation object 'selectPeaks':
  'good' 'bad' 'cleaned' 'best'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... WARNING
Argument items with no description in Rd object '.updateObject.RmbSpectrum2.formulaSource':
  'w'

* checking for unstated dependencies in examples ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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: 8 WARNINGs, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/RMassBank.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch RMassBank
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
* installing *source* package 'RMassBank' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RMassBank'
    finding HTML links ... done
    CTS.externalIdSubset                    html  
    CTS.externalIdTypes                     html  
    RmbDefaultSettings                      html  
    RmbSettings                             html  
    add.formula                             html  
    addMB                                   html  
    addPeaks                                html  
    addPeaksManually                        html  
    addProperty                             html  
    aggregateSpectra                        html  
    analyzeMsMs                             html  
    annotator.default                       html  
    archiveResults                          html  
    checkIsotopes                           html  
    checkSpectra                            html  
    cleanElnoise                            html  
    combineMultiplicities                   html  
    createMolfile                           html  
    dbe                                     html  
    deprofile                               html  
    dot-buildRecord.RmbSpectraSet           html  
    dot-parseTitleString                    html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/meat/RMassBank/man/dot-parseTitleString.Rd:38: missing link 'compileRecord'
    dot-updateObject.RmbSpectrum2.formulaSource
                                            html  
    exportMassbank                          html  
Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/meat/RMassBank/man/exportMassbank.Rd:11: missing link 'compileRecord'
Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/meat/RMassBank/man/exportMassbank.Rd:52: missing link 'compileRecord'
    fillback                                html  
    filterLowaccResults                     html  
    filterMultiplicity                      html  
    filterPeakSatellites                    html  
    filterPeaksMultiplicity                 html  
    findEIC                                 html  
    findMass                                html  
    findMsMsHR                              html  
    findMsMsHR.direct                       html  
    findMsMsHR.ticms2                       html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-RMassBank/00new/RMassBank/help/findMsMsHR.ticMS2.html
    findMsMsHRperxcms                       html  
    findMz                                  html  
    findMz.formula                          html  
    findProgress                            html  
    flatten                                 html  
    formulastring.to.list                   html  
    gatherData                              html  
    gatherDataBabel                         html  
    gatherDataUnknown                       html  
    gatherPubChem                           html  
    getAnalyticalInfo                       html  
Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/meat/RMassBank/man/getAnalyticalInfo.Rd:71: missing link 'compileRecord'
    getCSID                                 html  
    getCactus                               html  
    getCompTox                              html  
    getCtsKey                               html  
    getCtsRecord                            html  
    getData                                 html  
    getMolecule                             html  
    getPcId                                 html  
    is.valid.formula                        html  
    loadInfolists                           html  
    loadList                                html  
    makeMollist                             html  
    makePeaksCache                          html  
    makeRecalibration                       html  
    mbWorkflow                              html  
    mbWorkspace-class                       html  
    mergePeaks.df                           html  
    msmsRead.RAW                            html  
    msmsRead                                html  
    msmsWorkflow                            html  
    msmsWorkspace-class                     html  
    newMbWorkspace                          html  
    newMsmsWorkspace                        html  
    order.formula                           html  
    parseMassBank                           html  
    parseMbRecord                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-RMassBank/00new/RMassBank/help/parseMassBank.html
    peaksMatched                            html  
    peaksUnmatched                          html  
    plotMbWorkspaces                        html  
    plotRecalibration                       html  
    ppm                                     html  
    problematicPeaks                        html  
    processProblematicPeaks                 html  
    progressBarHook                         html  
    reanalyzeFailpeaks                      html  
    recalibrate                             html  
    recalibrate.addMS1data                  html  
    selectPeaks                             html  
    selectSpectra                           html  
    setData                                 html  
    smiles2mass                             html  
    spectraCount                            html  
    to.limits.rcdk                          html  
    toMassbank                              html  
Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/meat/RMassBank/man/toMassbank.Rd:79: missing link 'compileRecord'
    toRMB                                   html  
    updateSettings                          html  
    validate                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RMassBank)
Making 'packages.html' ... done

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #### doRUnit.R --- Run RUnit tests
> ####------------------------------------------------------------------------
> 
> ### Structure borrowed from rcppgls:
> ### https://github.com/eddelbuettel/rcppgsl/blob/master/tests/doRUnit.R
> 
> if(require("RUnit", quietly = TRUE)) {
+ 	if(require("RMassBankData", quietly = TRUE) && !(compareVersion(installed.packages()["RMassBankData","Version"],"1.99.0") == -1)) {
+ 		pkg <- "RMassBank"
+ 		print("Starting tests")
+ 		require(pkg, character.only=TRUE)
+ 
+ 		path <- system.file("unitTests", package = pkg)
+ 
+ 		stopifnot(file.exists(path), file.info(path.expand(path))$isdir)
+ 
+ 		source(file.path(path, "runTests.R"), echo = TRUE)
+ 	} else {
+ 		## Taking this message out until the new RMassBankData is on bioc, just to avoid confusion.
+         # message("Package RMassBankData with version > 1.99 not available, cannot run unit tests")
+ 	}
+ } else {
+ 	message("Package RUnit not available, cannot run unit tests")
+ }
NULL
> 
> proc.time()
   user  system elapsed 
   2.20    0.76    2.96