############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:RMassBank.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RMassBank_3.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RMassBank.Rcheck' * using R version 4.1.3 (2022-03-10) * 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 '3.4.0' * 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 ... 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-3.14-bioc/meat/RMassBank/man/dot-parseTitleString.Rd:38: missing link 'compileRecord' Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/meat/RMassBank/man/exportMassbank.Rd:11: missing link 'compileRecord' Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/meat/RMassBank/man/exportMassbank.Rd:52: missing link 'compileRecord' Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/meat/RMassBank/man/getAnalyticalInfo.Rd:71: missing link 'compileRecord' Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/meat/RMassBank/man/toMassbank.Rd:79: missing link 'compileRecord' See 'C:/Users/biocbuild/bbs-3.14-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 : : : no visible global function definition for 'points' createSpecsFromPeaklists: no visible global function definition for 'read.csv' deprofile.spline : : no visible global function definition for 'smooth.spline' deprofile.spline : : no visible global function definition for 'predict' findEIC: no visible global function definition for 'predict' findMsMsHRperxcms.direct : getRT : : 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 : : no visible binding for global variable 'filterOK' mbWorkflow : : no visible binding for global variable 'best' msmsRead: no visible global function definition for 'read.csv' msmsRead.RAW : getRT : : 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 : : 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' Undocumented arguments in documentation object 'msmsWorkflow' 'filetable' Documented arguments not in \usage in documentation object 'processProblematicPeaks': '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 ... 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 ... WARNING Found the following significant warnings: Warning: 'do.typing' is deprecated. Warning: 'do.typing' is deprecated. Warning: 'do.typing' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. * 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: 9 WARNINGs, 4 NOTEs See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RMassBank.Rcheck/00check.log' for details.