############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsBig.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsBig_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MSstatsBig.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MSstatsBig/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MSstatsBig’ version ‘1.3.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘MSstatsBig’ can be installed ... OK * 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 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE MSstatsPreprocessBig: no visible binding for global variable ‘input’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘PeptideSequence’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘PrecursorCharge’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘FragmentIon’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘ProductCharge’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘ProteinName’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘Feature’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘Intensity’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘MeanAbundance’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘feature_rank’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘NumProteins’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘IsotopeLabelType’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘Run’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘Condition’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘BioReplicate’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘NumObs’ MSstatsPreprocessBigSparklyr: no visible global function definition for ‘%>%’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘Condition’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘BioReplicate’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘PeptideSequence’ MSstatsPreprocessBigSparklyr: no visible global function definition for ‘n_distinct’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘ProteinName’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘NumProteins’ MSstatsPreprocessBigSparklyr: no visible global function definition for ‘tbl’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘PrecursorCharge’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘FragmentIon’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘ProductCharge’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘IsotopeLabelType’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘Run’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘Intensity’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘NumObs’ MSstatsPreprocessBigSparklyr: no visible global function definition for ‘min_rank’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘Rank’ cleanSpectronautChunk: no visible global function definition for ‘all_of’ cleanSpectronautChunk: no visible binding for global variable ‘Intensity’ cleanSpectronautChunk: no visible binding for global variable ‘Excluded’ cleanSpectronautChunk: no visible binding for global variable ‘Identified’ cleanSpectronautChunk: no visible binding for global variable ‘EGQvalue’ cleanSpectronautChunk: no visible binding for global variable ‘PGQvalue’ cleanSpectronautChunk: no visible binding for global variable ‘FFrgLossType’ cleanSpectronautChunk: no visible binding for global variable ‘LabeledSequence’ cleanSpectronautChunk: no visible global function definition for ‘:=’ cleanSpectronautChunk: no visible binding for global variable ‘IsotopeLabelType’ cleanSpectronautChunk: no visible binding for global variable ‘IsLabeled’ cleanSpectronautChunk: no visible binding for global variable ‘ProteinName’ cleanSpectronautChunk: no visible binding for global variable ‘PeptideSequence’ cleanSpectronautChunk: no visible binding for global variable ‘PrecursorCharge’ cleanSpectronautChunk: no visible binding for global variable ‘FragmentIon’ cleanSpectronautChunk: no visible binding for global variable ‘ProductCharge’ cleanSpectronautChunk: no visible binding for global variable ‘Run’ cleanSpectronautChunk: no visible binding for global variable ‘BioReplicate’ cleanSpectronautChunk: no visible binding for global variable ‘Condition’ Undefined global functions or variables: %>% := BioReplicate Condition EGQvalue Excluded FFrgLossType Feature FragmentIon Identified Intensity IsLabeled IsotopeLabelType LabeledSequence MeanAbundance NumObs NumProteins PGQvalue PeptideSequence PrecursorCharge ProductCharge ProteinName Rank Run all_of feature_rank input min_rank n_distinct tbl * 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 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MSstatsBig.Rcheck/00check.log’ for details.