############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:msPurity.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings msPurity_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/msPurity.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘msPurity/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘msPurity’ version ‘1.33.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘msPurity’ can be installed ... OK * checking installed package size ... INFO installed size is 12.7Mb sub-directories of 1Mb or more: extdata 12.0Mb * 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 loading without being on the library search path ... 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 177.936 5.178 149.463 frag4feature-purityA-method 153.725 5.716 125.869 flag_remove 33.184 6.661 20.233 dimsPredictPurity-purityD-method 30.071 1.370 31.444 purityX 30.102 0.293 30.391 combineAnnotations 8.895 0.099 8.998 assessPuritySingle 7.707 0.121 7.829 groupPeaks-purityD-method 6.377 1.312 7.690 purityA 7.040 0.044 7.084 spectralMatching 5.291 1.790 7.576 subtract-purityD-method 3.882 1.287 5.169 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/msPurity.Rcheck/00check.log’ for details.