############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsPTM_2.6.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MSstatsPTM.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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MSstatsPTM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MSstatsPTM’ version ‘2.6.1’ * 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 ... WARNING Found the following significant warnings: Warning: MSstatsPTM.Rd:3: docType ‘_PACKAGE’ is unrecognized See ‘/Users/biocbuild/bbs-3.19-bioc/meat/MSstatsPTM.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... NOTE Unexported objects imported by ':::' calls: ‘MSstats:::.getMedianSigmaSubject’ ‘MSstats:::.getVarComponent’ ‘MSstatsConvert:::.filterFewMeasurements’ ‘MSstatsConvert:::.filterManyColumns’ ‘MSstatsConvert:::.getChannelColumns’ ‘MSstatsConvert:::.standardizeColnames’ 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 .extract_pd_mods: no visible binding for global variable ‘..sequence_col’ .format.data.process.plots: no visible binding for global variable ‘ABUNDANCE’ .pivotPS: no visible binding for global variable ‘..keep_cols’ .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’ .removeCutoffSites: no visible binding for global variable ‘..mod_pep_col’ .rmConfounded: no visible binding for global variable ‘..col_res’ DIANNtoMSstatsPTMFormat: no visible binding for global variable ‘..protein_id_col’ FragPipetoMSstatsPTMFormat: no visible binding for global variable ‘..msstats_cols’ MSstatsPTMSiteLocator: no visible binding for global variable ‘..mod_pep_col’ MaxQtoMSstatsPTMFormat: no visible binding for global variable ‘TMT.keyword’ MaxQtoMSstatsPTMFormat: no visible binding for global variable ‘ptm.keyword’ MaxQtoMSstatsPTMFormat: no visible binding for global variable ‘mod.num’ MaxQtoMSstatsPTMFormat: no visible binding for global variable ‘which.proteinid.ptm’ MaxQtoMSstatsPTMFormat: no visible binding for global variable ‘PeptideSequence’ MetamorpheusToMSstatsPTMFormat: no visible binding for global variable ‘..protein_id_col’ PStoMSstatsPTMFormat: no visible binding for global variable ‘Intensity’ ProgenesistoMSstatsPTMFormat: no visible binding for global variable ‘Type’ SkylinetoMSstatsPTMFormat: no visible binding for global variable ‘annotation_prot’ 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 ..keep_cols ..mod_pep_col ..msstats_cols ..protein_id_col ..sequence_col ABUNDANCE GLOBALPROTEIN Intensity PROTEINNAME PeptideSequence TMT.keyword Type address annotation_prot mod.num ptm.keyword text.angle which.proteinid.ptm * checking Rd files ... WARNING prepare_Rd: MSstatsPTM.Rd:3: docType ‘_PACKAGE’ is unrecognized * 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-fixTerminus.Rd': ‘fasta_file’ 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 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 11.948 0.137 12.119 dataSummarizationPTM_TMT 6.960 0.384 5.603 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ 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 WARNINGs, 5 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/MSstatsPTM.Rcheck/00check.log’ for details.