############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:MSstatsConvert.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MSstatsConvert_1.19.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MSstatsConvert.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MSstatsConvert/DESCRIPTION’ ... OK * this is package ‘MSstatsConvert’ version ‘1.19.3’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘MSstatsConvert’ can be installed ... OK * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * checking installed package size ... INFO installed size is 8.6Mb sub-directories of 1Mb or more: libs 2.0Mb tinytest 6.1Mb * 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 whether startup messages can be suppressed ... 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 .checkAnomalySkew: no visible global function definition for ‘.’ .checkAnomalySkew: no visible binding for global variable ‘AnomalyScores’ .checkAnomalySkew: no visible binding for global variable ‘PSM’ .checkFeatureCoverage: no visible global function definition for ‘.’ .checkFeatureCoverage: no visible binding for global variable ‘Intensity’ .checkFeatureCoverage: no visible binding for global variable ‘Feature’ .checkFeatureOutliers: no visible binding for global variable ‘is_outlier’ .checkFeatureOutliers: no visible binding for global variable ‘Intensity’ .checkFeatureOutliers: no visible binding for global variable ‘mean_Intensity’ .checkFeatureOutliers: no visible binding for global variable ‘sd_Intensity’ .checkFeatureOutliers: no visible global function definition for ‘.’ .checkFeatureOutliers: no visible binding for global variable ‘Feature’ .checkFeatureSD: no visible global function definition for ‘.’ .checkFeatureSD: no visible global function definition for ‘sd’ .checkFeatureSD: no visible binding for global variable ‘Intensity’ .checkFeatureSD: no visible binding for global variable ‘Feature’ .checkIntensityDistribution: no visible global function definition for ‘sd’ .cleanDIANNAddMissingColumns: no visible binding for global variable ‘PrecursorMz’ .cleanDIANNAddMissingColumns: no visible binding for global variable ‘FragmentInfo’ .cleanDIANNCleanAndFilterData: no visible binding for global variable ‘FragmentIon’ .cleanDIANNProcessFragmentInfo: no visible binding for global variable ‘FragmentInfo’ .cleanDIANNProcessFragmentInfo: no visible binding for global variable ‘FragmentIon’ .cleanDIANNProcessFragmentInfo: no visible binding for global variable ‘ProductCharge’ .cleanDIANNProcessQuantificationColumns: no visible binding for global variable ‘FragmentQuantCorrected’ .cleanDIANNRenameColumns: no visible binding for global variable ‘PeptideSequence’ .cleanRawPhilosopher: no visible binding for global variable ‘Run’ .prepareSpectronautAnomalyInput: no visible binding for global variable ‘Intensity’ .prepareSpectronautAnomalyInput: no visible global function definition for ‘.’ .prepareSpectronautAnomalyInput: no visible binding for global variable ‘Fragment’ .prepareSpectronautAnomalyInput: no visible binding for global variable ‘count’ .prepareSpectronautAnomalyInput: no visible binding for global variable ‘ProteinName’ .prepareSpectronautAnomalyInput: no visible binding for global variable ‘feature_rank’ .prepareSpectronautAnomalyInput: no visible binding for global variable ‘MeanAbundance’ .prepareSpectronautAnomalyInput: no visible binding for global variable ‘..cols’ .prepareSpectronautAnomalyInput: no visible binding for global variable ‘PSM’ .prepareSpectronautAnomalyInput: no visible binding for global variable ‘Order’ .runAnomalyModel : : no visible binding for global variable ‘..quality_metrics’ .summarizeMultipleMeasurements: no visible binding for global variable ‘row_id’ .summarizeMultipleMeasurements: no visible global function definition for ‘.’ .summarizeMultiplePSMs: no visible binding for global variable ‘Purity’ .summarizeMultiplePSMs: no visible binding for global variable ‘PeptideProphet.Probability’ .validateMSstatsConverterParameters: no visible global function definition for ‘modifyList’ DIANNtoMSstatsFormat: no visible binding for global variable ‘DetectionQValue’ DIANNtoMSstatsFormat: no visible binding for global variable ‘LibPGQValue’ DIANNtoMSstatsFormat: no visible binding for global variable ‘LibQValue’ DIANNtoMSstatsFormat: no visible binding for global variable ‘GlobalPGQValue’ DIANNtoMSstatsFormat: no visible binding for global variable ‘GlobalQValue’ MSstatsAnomalyScores: no visible binding for global variable ‘..subset_cols’ SkylinetoMSstatsFormat: no visible binding for global variable ‘Intensity’ SpectronauttoMSstatsFormat: no visible binding for global variable ‘Intensity’ pearson_skewness: no visible global function definition for ‘sd’ MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global variable ‘Run’ Undefined global functions or variables: . ..cols ..quality_metrics ..subset_cols AnomalyScores DetectionQValue Feature Fragment FragmentInfo FragmentIon FragmentQuantCorrected GlobalPGQValue GlobalQValue Intensity LibPGQValue LibQValue MeanAbundance Order PSM PeptideProphet.Probability PeptideSequence PrecursorMz ProductCharge ProteinName Purity Run count feature_rank is_outlier mean_Intensity modifyList row_id sd sd_Intensity Consider adding importFrom("stats", "sd") importFrom("utils", "modifyList") 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 ... NOTE Documented arguments not in \usage in Rd file 'dot-getFullDesign.Rd': ‘`feature_col`’ ‘`measurement_col`’ Documented arguments not in \usage in Rd file 'dot-mergeAnnotation.Rd': ‘data.table’ Documented arguments not in \usage in Rd file 'dot-sharedParametersAmongConverters.Rd': ‘removeFewMeasurements’ ‘useUniquePeptide’ ‘summaryforMultipleRows’ ‘removeProtein_with1Feature’ ‘removeProtein_with1Peptide’ ‘removeOxidationMpeptides’ ‘removeMpeptides’ ‘use_log_file’ ‘append’ ‘verbose’ ‘log_file_path’ ‘...’ 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 ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘tinytest.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: 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/MSstatsConvert.Rcheck/00check.log’ for details.