############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:msPurity.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings msPurity_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/msPurity.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'msPurity/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'msPurity' version '1.32.0' * package encoding: UTF-8 * checking package namespace information ... NOTE Found export directive that requires package 'methods': 'exportMethods' Remove all such namespace directives (if obsolete) or ensure that the DESCRIPTION Depends or Imports field contains 'methods'. * 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 whether package 'msPurity' can be installed ... OK * checking installed package size ... NOTE installed size is 19.6Mb sub-directories of 1Mb or more: extdata 18.8Mb * 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 code 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 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. package 'methods' is used but not declared * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE addGenericMS1LookupResults: no visible global function definition for 'count.fields' addMetFragResults: no visible global function definition for 'count.fields' addSiriusResults: no visible global function definition for 'count.fields' assessPuritySingle: no visible binding for global variable 'parallel' combineAnnotations: no visible binding for global variable 'compoundDbname' createDatabase: no visible global function definition for 'featureValues' create_database : getxcmsSetObject: no visible global function definition for 'sampclass<-' dimsPredictPuritySingleMz: no visible binding for global variable 'mtchi' dimsPredictPuritySingleMz: no visible binding for global variable 'alli' dimsPredictPuritySingleMz: no visible binding for global variable 'mtch' filterPrecursors: no visible binding for global variable 'l_speakmetaFiltered' filterSMeta: no visible binding for global variable 'accession' filterSMeta: no visible binding for global variable 'inPurity' filterSMeta: no visible global function definition for 'lower' filterSMeta: no visible binding for global variable 'polarity' filterSMeta: no visible binding for global variable 'instrument_type' filterSMeta: no visible binding for global variable 'instrument' filterSMeta: no visible binding for global variable 'name.y' filterSMeta: no visible binding for global variable 'retention_time' filterSMeta: no visible binding for global variable 'grpid' filterSMeta: no visible binding for global variable 'pid' filterSMeta: no visible binding for global variable 'spectrum_type' flag_remove: no visible global function definition for 'PeakDensityParam' flag_remove: no visible global function definition for 'chromPeaks<-' flag_remove: no visible global function definition for 'chromPeaks' getScanPeaksSqlite: no visible binding for global variable 'pid' getScanPeaksSqlite: no visible binding for global variable 'library_spectra_meta_id' getScanPeaksSqlite: no visible binding for global variable 'pass_flag' getScanPeaksSqlite: no visible binding for global variable 'type' getScanPeaksSqlite: no visible binding for global variable 'spectraType' getScanPeaksSqlite: no visible binding for global variable 'ra' getSmeta: no visible binding for global variable 'pid' get_topn: no visible binding for global variable 'topn' matchi: no visible global function definition for 'match_factor' plotPurity: no visible binding for global variable 'idx' plotPurity: no visible binding for global variable 'purity' plotPurity: no visible binding for global variable 'variable' purityA: no visible binding for global variable 'i' queryVlibrary: no visible binding for global variable 'precursor_mz' queryVlibrary: no visible binding for global variable 'retention_time' queryVlibrarySingle: no visible binding for global variable 'pid' queryVlibrarySingle: no visible binding for global variable 'library_spectra_meta_id' sum_calc_peaklist: no visible global function definition for 'phenoData' averageSpectra,purityD: no visible binding for global variable 'i' subtract,purityD: no visible binding for global variable 'i' Undefined global functions or variables: PeakDensityParam accession alli chromPeaks chromPeaks<- compoundDbname count.fields featureValues grpid i idx inPurity instrument instrument_type l_speakmetaFiltered library_spectra_meta_id lower match_factor mtch mtchi name.y parallel pass_flag phenoData pid polarity precursor_mz purity ra retention_time sampclass<- spectraType spectrum_type topn type variable Consider adding importFrom("utils", "count.fields") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) createMSP-purityA-method.Rd:25: Lost braces; missing escapes or markup? 25 | \item{msp_file_pth}{character; Name of the output msp file, if NULL the file "frag_spectra_{time stamp}.msp" will be created in the current directory} | ^ * 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 files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed createDatabase 142.83 2.41 267.69 frag4feature-purityA-method 112.62 1.03 236.90 purityX 45.02 5.75 51.14 dimsPredictPurity-purityD-method 39.61 1.66 41.27 flag_remove 12.78 0.42 47.09 combineAnnotations 12.28 0.66 12.97 assessPuritySingle 9.89 0.23 10.29 spectralMatching 6.64 3.29 22.08 purityA 9.33 0.18 9.51 groupPeaks-purityD-method 7.77 1.22 9.04 subtract-purityD-method 6.09 1.21 7.31 groupPeaksEx 5.31 1.00 6.31 averageSpectra-purityD-method 4.52 1.07 5.61 filterp-purityD-method 4.37 1.06 5.44 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 6 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/msPurity.Rcheck/00check.log' for details.