############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MSstatsPTM_1.4.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/MSstatsPTM.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MSstatsPTM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MSstatsPTM’ version ‘1.4.2’ * 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 ... NOTE Found the following hidden files and directories: .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 ‘MSstatsPTM’ 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 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .format.data.process.plots: no visible binding for global variable ‘ABUNDANCE’ .plot.model.volcano: no visible binding for global variable ‘text.angle’ .progensis.add.sites: no visible binding for global variable ‘..col_order’ .qc.all.plot.lf: no visible binding for global variable ‘text.angle’ .qc.single.plot.lf: no visible binding for global variable ‘text.angle’ .rmConfounded: no visible binding for global variable ‘..col_res’ MaxQtoMSstatsPTMFormat: no visible binding for global variable ‘PeptideSequence’ ProgenesistoMSstatsPTMFormat: no visible binding for global variable ‘Type’ SpectronauttoMSstatsPTMFormat: no visible binding for global variable ‘R.Condition’ SpectronauttoMSstatsPTMFormat: no visible binding for global variable ‘join_PeptideSequence’ SpectronauttoMSstatsPTMFormat: no visible binding for global variable ‘PeptideSequence’ dataProcessPlotsPTM: no visible binding for global variable ‘PROTEINNAME’ dataProcessPlotsPTM: no visible binding for global variable ‘GLOBALPROTEIN’ dataSummarizationPTM: no visible binding for global variable ‘address’ locatePTM: no visible binding for global variable ‘..col_seq’ locatePTM: no visible binding for global variable ‘..col_fasta’ Undefined global functions or variables: ..col_fasta ..col_order ..col_res ..col_seq ABUNDANCE GLOBALPROTEIN PROTEINNAME PeptideSequence R.Condition Type address join_PeptideSequence text.angle * 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 groupComparisonPlotsPTM 10.381 0.096 10.467 groupComparisonPTM 5.189 0.140 5.321 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘tinytest.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: 3 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/MSstatsPTM.Rcheck/00check.log’ for details.