############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msPurity.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msPurity_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/msPurity.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘msPurity/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘msPurity’ version ‘1.18.0’ * 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: .git_fetch_output.txt .git_merge_output.txt .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 ... NOTE installed size is 12.5Mb sub-directories of 1Mb or more: extdata 11.8Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ...It is recommended to use ‘given’ instead of ‘middle’. It is recommended to use ‘given’ instead of ‘middle’. NOTE Authors@R field gives persons with no role: Mark ths Viant Warwick ths Dunn * 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 ... WARNING Namespaces in Imports field not imported from: ‘dbplyr’ ‘jsonlite’ ‘uuid’ All declared Imports should be used. 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. Missing or unexported object: ‘stats::mean’ 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’ 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’ 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’ getxcmsSetObject: no visible global function definition for ‘sampclass<-’ 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’ averageSpectra,purityD: no visible binding for global variable ‘i’ subtract,purityD: no visible binding for global variable ‘i’ Undefined global functions or variables: accession alli compoundDbname count.fields grpid i idx inPurity instrument instrument_type l_speakmetaFiltered library_spectra_meta_id lower match_factor mtch mtchi name.y parallel pass_flag 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 ... OK * 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 frag4feature-purityA-method 62.087 3.478 60.971 dimsPredictPurity-purityD-method 51.056 0.441 51.543 flag_remove 26.904 7.047 18.000 purityX 17.667 4.739 14.983 combineAnnotations 16.189 0.298 16.499 purityA 14.499 0.065 14.576 assessPuritySingle 13.781 0.093 13.889 createDatabase 12.750 0.529 13.295 spectralMatching 7.859 1.881 10.446 groupPeaks-purityD-method 7.807 0.866 8.683 subtract-purityD-method 5.974 0.640 6.625 groupPeaksEx 5.519 0.306 5.831 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 1 WARNING, 4 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/msPurity.Rcheck/00check.log’ for details.