############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MSstatsShiny.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MSstatsShiny_1.6.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MSstatsShiny.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘MSstatsShiny/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MSstatsShiny’ version ‘1.6.2’ * 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 ‘MSstatsShiny’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘MSstats::SkylinetoMSstatsFormat’ by ‘MSstatsConvert::SkylinetoMSstatsFormat’ when loading ‘MSstatsShiny’ Warning: replacing previous import ‘MSstats::ProgenesistoMSstatsFormat’ by ‘MSstatsConvert::ProgenesistoMSstatsFormat’ when loading ‘MSstatsShiny’ Warning: replacing previous import ‘MSstats::SpectronauttoMSstatsFormat’ by ‘MSstatsConvert::SpectronauttoMSstatsFormat’ when loading ‘MSstatsShiny’ Warning: replacing previous import ‘MSstats::FragPipetoMSstatsFormat’ by ‘MSstatsConvert::FragPipetoMSstatsFormat’ when loading ‘MSstatsShiny’ Warning: replacing previous import ‘MSstats::DIAUmpiretoMSstatsFormat’ by ‘MSstatsConvert::DIAUmpiretoMSstatsFormat’ when loading ‘MSstatsShiny’ Warning: replacing previous import ‘MSstats::OpenMStoMSstatsFormat’ by ‘MSstatsConvert::OpenMStoMSstatsFormat’ when loading ‘MSstatsShiny’ Warning: replacing previous import ‘MSstats::MaxQtoMSstatsFormat’ by ‘MSstatsConvert::MaxQtoMSstatsFormat’ when loading ‘MSstatsShiny’ Warning: replacing previous import ‘MSstats::PDtoMSstatsFormat’ by ‘MSstatsConvert::PDtoMSstatsFormat’ when loading ‘MSstatsShiny’ Warning: replacing previous import ‘MSstats::OpenSWATHtoMSstatsFormat’ by ‘MSstatsConvert::OpenSWATHtoMSstatsFormat’ when loading ‘MSstatsShiny’ Warning: replacing previous import ‘MSstats::DIANNtoMSstatsFormat’ by ‘MSstatsConvert::DIANNtoMSstatsFormat’ when loading ‘MSstatsShiny’ See ‘/home/biocbuild/bbs-3.19-bioc/meat/MSstatsShiny.Rcheck/00install.out’ for details. * 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘shinyBS:::buildTooltipOrPopoverOptionsList’ ‘shinyBS:::shinyBSDep’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE getAnnot: no visible binding for global variable ‘annotation.pd’ getSummary1: no visible binding for global variable ‘Condition’ getSummary1: no visible binding for global variable ‘BioReplicate’ getSummary1: no visible binding for global variable ‘Mixture’ getSummary1: no visible binding for global variable ‘Run’ getSummary1: no visible binding for global variable ‘TechRepMixture’ getSummary1: no visible binding for global variable ‘Fraction’ getSummary1: no visible binding for global variable ‘Condition_Run’ getSummary1: no visible binding for global variable ‘BioReplicate_Run’ getSummary1: no visible binding for global variable ‘Number of Fractions’ getSummary2: no visible binding for global variable ‘ProteinName’ getSummary2: no visible binding for global variable ‘PeptideSequence’ getSummary2: no visible binding for global variable ‘Charge’ getSummary2: no visible binding for global variable ‘PrecursorCharge’ getSummary2: no visible binding for global variable ‘FragmentIon’ getSummary2: no visible binding for global variable ‘ProductCharge’ getSummary2: no visible binding for global variable ‘FEATURES’ getSummary2: no visible binding for global variable ‘Intensity’ getSummary2: no visible binding for global variable ‘Min_Intensity’ getSummary2: no visible binding for global variable ‘Max_Intensity’ getSummary2: no visible binding for global variable ‘npep’ getSummary2: no visible binding for global variable ‘nfea’ getSummary2: no visible binding for global variable ‘Features_Peptides_min’ getSummary2: no visible binding for global variable ‘Features_Peptides_max’ getSummary2: no visible binding for global variable ‘Peptides_Proteins_min’ getSummary2: no visible binding for global variable ‘Peptides_Proteins_max’ loadpageServer: no visible global function definition for ‘moduleServer’ server: no visible global function definition for ‘callModule’ statmodelServer: no visible global function definition for ‘updateNumericInput’ Undefined global functions or variables: BioReplicate BioReplicate_Run Charge Condition Condition_Run FEATURES Features_Peptides_max Features_Peptides_min Fraction FragmentIon Intensity Max_Intensity Min_Intensity Mixture Number of Fractions PeptideSequence Peptides_Proteins_max Peptides_Proteins_min PrecursorCharge ProductCharge ProteinName Run TechRepMixture annotation.pd callModule moduleServer nfea npep updateNumericInput * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed tmt_model 6.930 0.144 5.980 tmt_summarization_loop 6.853 0.031 5.778 apply_adj 5.577 0.260 5.831 lf_summarization_loop 4.873 0.851 4.975 * 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: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/MSstatsShiny.Rcheck/00check.log’ for details.