############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:sangeranalyseR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings sangeranalyseR_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/sangeranalyseR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sangeranalyseR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sangeranalyseR’ version ‘1.2.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'stringr', 'ape', 'Biostrings', 'DECIPHER', 'parallel', 'reshape2', 'phangorn', 'sangerseqR', 'gridExtra', 'shiny', 'shinydashboard', 'shinyjs', 'data.table', 'plotly', 'DT', 'zeallot', 'excelR', 'shinycssloaders', 'ggdendro', 'shinyWidgets', 'openxlsx', 'tools', 'rmarkdown', 'kableExtra', 'seqinr', 'BiocStyle', 'logger' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 docs/build/html/.buildinfo These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... WARNING Found the following file with a non-portable file name: docs/wallpaperflare.com_wallpaper (1).jpg These are not fully portable file names. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for sufficient/correct file permissions ... OK * checking whether package ‘sangeranalyseR’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.7Mb sub-directories of 1Mb or more: extdata 4.1Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... WARNING Found the following files with non-ASCII characters: ClassSangerAlignment.R ClassSangerContig.R ClassSangerRead.R Portable packages must use only ASCII characters in their R code, except perhaps in comments. Use \uxxxx escapes for other characters. * 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 Packages in Depends field not imported from: ‘BiocStyle’ ‘phangorn’ ‘reshape2’ ‘zeallot’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. package 'methods' is used but not declared * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE SangerAlignment: no visible global function definition for ‘new’ SangerAlignmentServer: no visible binding for '<<-' assignment to ‘NEW_SANGER_ALIGNED_CONSENSUS_READ_SET’ SangerAlignmentServer: no visible global function definition for ‘colorRamp’ SangerContig: no visible global function definition for ‘new’ SangerContigServer: no visible binding for '<<-' assignment to ‘NEW_SANGER_CONTIG’ SangerContigServer: no visible global function definition for ‘colorRamp’ SangerRead: no visible global function definition for ‘new’ alignContigs: no visible global function definition for ‘as.phylo’ alignContigs: no visible global function definition for ‘rtree’ checkAb1FastaCsv: no visible global function definition for ‘read.csv’ chromatogram_overwrite: no visible global function definition for ‘rgb’ chromatogram_overwrite: no visible global function definition for ‘par’ chromatogram_overwrite: no visible global function definition for ‘quantile’ chromatogram_overwrite: no visible global function definition for ‘IQR’ chromatogram_overwrite: no visible global function definition for ‘pdf’ chromatogram_overwrite: no visible global function definition for ‘rect’ chromatogram_overwrite: no visible global function definition for ‘lines’ chromatogram_overwrite: no visible global function definition for ‘mtext’ chromatogram_overwrite: no visible global function definition for ‘axis’ chromatogram_overwrite: no visible global function definition for ‘dev.off’ primarySeqDisplay: no visible global function definition for ‘rgb’ primarySeqTrimmedDisplay: no visible global function definition for ‘rgb’ secondSeqTrimmedDisplay: no visible global function definition for ‘rgb’ secondarySeqDisplay: no visible global function definition for ‘rgb’ initialize,ChromatogramParam: no visible global function definition for ‘callNextMethod’ initialize,QualityReport: no visible global function definition for ‘callNextMethod’ initialize,SangerAlignment: no visible global function definition for ‘str_split’ initialize,SangerAlignment : : no visible global function definition for ‘new’ initialize,SangerAlignment: no visible global function definition for ‘read.csv’ initialize,SangerAlignment: no visible global function definition for ‘callNextMethod’ initialize,SangerContig: no visible global function definition for ‘read.csv’ initialize,SangerContig : : no visible global function definition for ‘new’ initialize,SangerContig: no visible global function definition for ‘callNextMethod’ initialize,SangerRead: no visible global function definition for ‘new’ initialize,SangerRead: no visible global function definition for ‘isEmpty’ initialize,SangerRead: no visible global function definition for ‘callNextMethod’ launchAppSA,SangerAlignment: no visible global function definition for ‘shinyOptions’ launchAppSA,SangerAlignment: no visible global function definition for ‘shinyApp’ launchAppSC,SangerContig: no visible global function definition for ‘shinyOptions’ launchAppSC,SangerContig: no visible global function definition for ‘shinyApp’ Undefined global functions or variables: IQR as.phylo axis callNextMethod colorRamp dev.off isEmpty lines mtext new par pdf quantile read.csv rect rgb rtree shinyApp shinyOptions str_split Consider adding importFrom("grDevices", "colorRamp", "dev.off", "pdf", "rgb") importFrom("graphics", "axis", "lines", "mtext", "par", "rect") importFrom("methods", "callNextMethod", "new") importFrom("stats", "IQR", "quantile") importFrom("utils", "read.csv") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'readTable' and siglist 'SangerContig' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'SangerAlignment-class-generateReportSA': \S4method{generateReportSA}{SangerAlignment} Code: function(object, outputDir, includeSangerContig = TRUE, includeSangerRead = TRUE, colors) Docs: function(object, outputDir, includeSangerContig = TRUE, includeSangerRead = TRUE) Argument names in code not in docs: colors Codoc mismatches from documentation object 'SangerAlignment-class-launchAppSA': \S4method{launchAppSA}{SangerAlignment} Code: function(object, outputDir = NULL, colors = "default") Docs: function(object, outputDir = NULL) Argument names in code not in docs: colors Codoc mismatches from documentation object 'SangerContig-class-generateReportSC': \S4method{generateReportSC}{SangerContig} Code: function(object, outputDir, includeSangerRead = TRUE, colors, navigationAlignmentFN = NULL) Docs: function(object, outputDir, includeSangerRead = TRUE, navigationAlignmentFN = NULL) Argument names in code not in docs: colors Mismatches in argument names: Position: 4 Code: colors Docs: navigationAlignmentFN Codoc mismatches from documentation object 'SangerContig-class-launchAppSC': \S4method{launchAppSC}{SangerContig} Code: function(object, outputDir = NULL, colors = "default") Docs: function(object, outputDir = NULL) Argument names in code not in docs: colors Codoc mismatches from documentation object 'SangerRead-class-generateReportSR': \S4method{generateReportSR}{SangerRead} Code: function(object, outputDir, colors, navigationContigFN = NULL, navigationAlignmentFN = NULL) Docs: function(object, outputDir, navigationContigFN = NULL, navigationAlignmentFN = NULL) Argument names in code not in docs: colors Mismatches in argument names: Position: 3 Code: colors Docs: navigationContigFN Position: 4 Code: navigationContigFN Docs: navigationAlignmentFN Codoc mismatches from documentation object 'generateReport': generateReport Code: function(object, outputDir = NULL, includeSangerContig = TRUE, includeSangerRead = TRUE, colors = "default", ...) Docs: function(object, outputDir = NULL, includeSangerContig = TRUE, includeSangerRead = TRUE, ...) Argument names in code not in docs: colors Mismatches in argument names: Position: 5 Code: colors Docs: ... Codoc mismatches from documentation object 'generateReportSA': generateReportSA Code: function(object, outputDir = NULL, includeSangerContig = TRUE, includeSangerRead = TRUE, colors = "default", ...) Docs: function(object, outputDir = NULL, includeSangerContig = TRUE, includeSangerRead = TRUE, ...) Argument names in code not in docs: colors Mismatches in argument names: Position: 5 Code: colors Docs: ... Codoc mismatches from documentation object 'generateReportSC': generateReportSC Code: function(object, outputDir = NULL, includeSangerRead = TRUE, colors = "default", ...) Docs: function(object, outputDir = NULL, includeSangerRead = TRUE, ...) Argument names in code not in docs: colors Mismatches in argument names: Position: 4 Code: colors Docs: ... Codoc mismatches from documentation object 'generateReportSR': generateReportSR Code: function(object, outputDir = NULL, colors = "default", ...) Docs: function(object, outputDir = NULL, ...) Argument names in code not in docs: colors Mismatches in argument names: Position: 3 Code: colors Docs: ... Codoc mismatches from documentation object 'launchApp': launchApp Code: function(object, outputDir = NULL, colors = "default") Docs: function(object, outputDir = NULL) Argument names in code not in docs: colors Codoc mismatches from documentation object 'launchAppSA': launchAppSA Code: function(object, outputDir = NULL, colors = "default") Docs: function(object, outputDir = NULL) Argument names in code not in docs: colors Codoc mismatches from documentation object 'launchAppSC': launchAppSC Code: function(object, outputDir = NULL, colors = "default") Docs: function(object, outputDir = NULL) Argument names in code not in docs: colors * 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 line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed SangerAlignment-class 39.445 6.931 41.171 SangerAlignment 10.085 1.741 10.534 SangerContig-class 9.240 1.811 9.719 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 4 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/sangeranalyseR.Rcheck/00check.log’ for details.