############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:MSstatsLiP.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings MSstatsLiP_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MSstatsLiP.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MSstatsLiP/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MSstatsLiP’ version ‘1.10.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘MSstatsLiP’ can be installed ... OK * used C++ compiler: ‘g++ (GCC) 10.3.1’ * 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 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 ResistanceBarcodePlotLiP: no visible binding for global variable ‘GROUP’ ResistanceBarcodePlotLiP: no visible binding for global variable ‘Protein’ ResistanceBarcodePlotLiP: no visible binding for global variable ‘uniprot_iso’ ResistanceBarcodePlotLiP: no visible binding for global variable ‘PeptideSequence’ ResistanceBarcodePlotLiP: no visible binding for global variable ‘Accessibility_ratio’ ResistanceBarcodePlotLiP: no visible binding for global variable ‘Index’ ResistanceBarcodePlotLiP: no visible binding for global variable ‘Label’ ResistanceBarcodePlotLiP: no visible binding for global variable ‘sig’ ResistanceBarcodePlotLiP: no visible binding for global variable ‘Coverage’ StructuralBarcodePlotLiP: no visible binding for global variable ‘NSEMI_TRI’ StructuralBarcodePlotLiP: no visible binding for global variable ‘CSEMI_TRI’ calculateProteolyticResistance: no visible binding for global variable ‘LogIntensities’ calculateProteolyticResistance: no visible binding for global variable ‘Protein.y’ Undefined global functions or variables: Accessibility_ratio CSEMI_TRI Coverage GROUP Index Label LogIntensities NSEMI_TRI PeptideSequence Protein Protein.y sig uniprot_iso * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed dataProcessPlotsLiP 30.683 0.287 31.039 StructuralBarcodePlotLiP 4.987 0.096 5.098 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/MSstatsLiP.Rcheck/00check.log’ for details.