##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:RMassBank.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings RMassBank_3.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/RMassBank.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘RMassBank/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RMassBank’ version ‘3.8.0’
* 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:
  .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 for sufficient/correct file permissions ... OK
* checking whether package ‘RMassBank’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘MSnbase::header’ by ‘R.utils::header’ when loading ‘RMassBank’
  Warning: replacing previous import ‘R.utils::reset’ by ‘RCurl::reset’ when loading ‘RMassBank’
  Warning: replacing previous import ‘R.utils::header’ by ‘mzR::header’ when loading ‘RMassBank’
See ‘/home/biocbuild/bbs-3.16-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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘ChemmineOB’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘MSnbase:::writeMgfContent’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* 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’
compoundlist2SDF: no visible binding for global variable ‘ID’
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’
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:
  ID 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  ‘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 'cleanElnoise' and siglist 'RmbSpectraSet,numeric,numeric'
  generic 'cleanElnoise' and siglist 'RmbSpectrum2,numeric,numeric'
  generic 'cleanElnoise' and siglist 'data.frame,numeric,numeric'
  generic 'normalize' and siglist 'RmbSpectrum2'
  generic 'normalize' and siglist 'RmbSpectrum2List'
  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 'getAnalyticalInfo' but not in code:
  ‘gatherCompound’ ‘gatherSpectrum’

Functions or methods with usage in documentation object 'getCompTox' but not in code:
  ‘getCompTox’

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 'makeRecalibration':
makeRecalibration
  Code: function(w, recalibrateBy =
                 getOption("RMassBank")$recalibrateBy, recalibrateMS1 =
                 getOption("RMassBank")$recalibrateMS1, recalibrator =
                 getOption("RMassBank")$recalibrator,
                 recalibrateMS1Window =
                 getOption("RMassBank")$recalibrateMS1Window)
  Docs: function(w, mode, recalibrateBy =
                 getOption("RMassBank")$recalibrateBy, recalibrateMS1 =
                 getOption("RMassBank")$recalibrateMS1, recalibrator =
                 getOption("RMassBank")$recalibrator,
                 recalibrateMS1Window =
                 getOption("RMassBank")$recalibrateMS1Window)
  Argument names in docs not in code:
    mode
  Mismatches in argument names (first 3):
    Position: 2 Code: recalibrateBy Docs: mode
    Position: 3 Code: recalibrateMS1 Docs: recalibrateBy
    Position: 4 Code: recalibrator Docs: recalibrateMS1
recalibrateSpectra
  Code: function(rawspec = NULL, rc = NULL, rc.ms1 = NULL, w = NULL,
                 recalibrateBy = getOption("RMassBank")$recalibrateBy,
                 recalibrateMS1 =
                 getOption("RMassBank")$recalibrateMS1)
  Docs: function(mode, rawspec = NULL, rc = NULL, rc.ms1 = NULL, w =
                 NULL, recalibrateBy =
                 getOption("RMassBank")$recalibrateBy, recalibrateMS1 =
                 getOption("RMassBank")$recalibrateMS1)
  Argument names in docs not in code:
    mode
  Mismatches in argument names (first 3):
    Position: 1 Code: rawspec Docs: mode
    Position: 2 Code: rc Docs: rawspec
    Position: 3 Code: rc.ms1 Docs: rc

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, 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 mode
  Mismatches in argument names:
    Position: 1 Code: w Docs: aggregated
    Position: 3 Code: filterSettings Docs: mode
    Position: 4 Code: progressbar Docs: filterSettings
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 'recalibrate.addMS1data':
recalibrate.addMS1data
  Code: function(spec, recalibrateMS1Window =
                 getOption("RMassBank")$recalibrateMS1Window)
  Docs: function(spec, mode = "pH", recalibrateMS1Window =
                 getOption("RMassBank")$recalibrateMS1Window)
  Argument names in docs not in code:
    mode
  Mismatches in argument names:
    Position: 2 Code: recalibrateMS1Window Docs: mode

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

S4 class codoc mismatches from documentation object 'RmbSpectrum2-class':
Slots for class 'RmbSpectrum2'
  Code: .__classVersion__ acquisitionNum centroided collisionEnergy dbe
        dppm dppmBest formula formulaCount formulaSource fromFile good
        info intensity low merged msLevel mz mzCalc ok peaksCount
        polarity precScanNum precursorCharge precursorIntensity
        precursorMz properties rawOK rt satellite scanIndex smoothed
        tic
  Inherited: merged precScanNum precursorMz precursorIntensity
        precursorCharge collisionEnergy msLevel peaksCount rt
        acquisitionNum scanIndex tic mz intensity fromFile centroided
        smoothed polarity .__classVersion__
  Docs: dbe dppm dppmBest formula formulaCount formulaSource good info
        low mzCalc ok properties rawOk satellite

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'buildRecord'
  ‘analyticalInfo’

Undocumented arguments in documentation object 'exportMassbank'
  ‘files’

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

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

Undocumented arguments in documentation object 'makeRecalibration'
  ‘mode’

Undocumented arguments in documentation object 'msmsWorkflow'
  ‘filetable’

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

Undocumented arguments in documentation object 'reanalyzeFailpeaks'
  ‘mode’

Undocumented arguments in documentation object 'recalibrate.addMS1data'
  ‘mode’

Undocumented arguments in documentation object 'rmb_log_debug'
  ‘...’

Undocumented arguments in documentation object 'rmb_log_error'
  ‘...’

Undocumented arguments in documentation object 'rmb_log_fatal'
  ‘...’

Undocumented arguments in documentation object 'rmb_log_info'
  ‘...’

Undocumented arguments in documentation object 'rmb_log_success'
  ‘...’

Undocumented arguments in documentation object 'rmb_log_trace'
  ‘...’

Undocumented arguments in documentation object 'rmb_log_warn'
  ‘...’

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 ... OK
* 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 ...
  ‘RMassBank.Rmd’ using ‘UTF-8’... OK
  ‘RMassBankNonstandard.Rmd’ using ‘UTF-8’... OK
  ‘RMassBankXCMS.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/RMassBank.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL RMassBank
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘RMassBank’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘MSnbase::header’ by ‘R.utils::header’ when loading ‘RMassBank’
Warning: replacing previous import ‘R.utils::reset’ by ‘RCurl::reset’ when loading ‘RMassBank’
Warning: replacing previous import ‘R.utils::header’ by ‘mzR::header’ when loading ‘RMassBank’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘MSnbase::header’ by ‘R.utils::header’ when loading ‘RMassBank’
Warning: replacing previous import ‘R.utils::reset’ by ‘RCurl::reset’ when loading ‘RMassBank’
Warning: replacing previous import ‘R.utils::header’ by ‘mzR::header’ when loading ‘RMassBank’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘MSnbase::header’ by ‘R.utils::header’ when loading ‘RMassBank’
Warning: replacing previous import ‘R.utils::reset’ by ‘RCurl::reset’ when loading ‘RMassBank’
Warning: replacing previous import ‘R.utils::header’ by ‘mzR::header’ when loading ‘RMassBank’
** testing if installed package keeps a record of temporary installation path
* DONE (RMassBank)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  1.160   0.131   1.276