############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sangeranalyseR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sangeranalyseR_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/sangeranalyseR.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sangeranalyseR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sangeranalyseR’ version ‘1.17.0’ * package encoding: UTF-8 * checking package namespace information ... NOTE Found export directives that require package ‘methods’: ‘exportClasses’ ‘exportMethods’ Remove all such namespace directives (if obsolete) or ensure that the DESCRIPTION Depends or Imports field contains ‘methods’. * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' INFO Depends: includes the non-default packages: 'stringr', 'ape', 'Biostrings', 'pwalign', 'DECIPHER', 'parallel', 'reshape2', 'sangerseqR', 'gridExtra', 'shiny', 'shinydashboard', 'shinyjs', 'data.table', 'plotly', 'DT', 'zeallot', 'excelR', 'shinycssloaders', 'ggdendro', 'shinyWidgets', 'openxlsx', 'tools', 'rmarkdown', 'knitr', '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. Found the following non-portable file paths: sangeranalyseR/docs/build/html/_downloads/081987116457968e1b81ae1616525c7d/Sanger_contigs_unalignment.fa sangeranalyseR/docs/build/html/_downloads/13b875bc704f73b8bd67dc07d86fc474/Sanger_contigs_alignment.fa sangeranalyseR/docs/build/html/_downloads/144d09562ae5b2c7dc079e4bc2b33fb7/Sanger_contigs_alignment.fa sangeranalyseR/docs/build/html/_downloads/165af37e8893cfdfa4dba91c44cd791b/Sanger_contigs_unalignment.fa sangeranalyseR/docs/build/html/_downloads/345ac400befc4f176c75732770ec3fcb/Achl_RBNII384-13_contig.fa sangeranalyseR/docs/build/html/_downloads/438c8bd47d93d92c65b35b613ef14739/Sanger_all_trimmed_reads.fa sangeranalyseR/docs/build/html/_downloads/6211ea1e7e3ccc1fcc9b74b78224eab6/Achl_ACHLO006-09_reads_unalignment.fa sangeranalyseR/docs/build/html/_downloads/67bcad64cca804ec2e14cc42d016c08f/Achl_ACHLO006-09_reads_alignment.fa sangeranalyseR/docs/build/html/_downloads/81a7338101f110748cb72056d9975225/Sanger_all_trimmed_reads.fa sangeranalyseR/docs/build/html/_downloads/95ef9378c1407481d69c3bf882a580bb/Achl_RBNII384-13_reads_unalignment.fa sangeranalyseR/docs/build/html/_downloads/a664bed9cc5d32924dc2ce60f8c60554/Sanger_all_trimmed_reads.fa sangeranalyseR/docs/build/html/_downloads/b608796fffaaa7335a7341cffc9a9db7/Achl_ACHLO006-09_contig.fa sangeranalyseR/docs/build/html/_downloads/b6b18aa3e34c6ae0be86c3940972dd38/Sanger_contigs_alignment.fa sangeranalyseR/docs/build/html/_downloads/eeb554b575ee5b29ef733dafbf876c36/Achl_RBNII384-13_reads_alignment.fa sangeranalyseR/docs/build/html/_downloads/fef71e7b2e1e49c01df301435e972047/Sanger_contigs_unalignment.fa Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. 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 ... INFO installed size is 8.5Mb sub-directories of 1Mb or more: data 2.2Mb extdata 5.5Mb * 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 code files for non-ASCII characters ... WARNING Found the following files with non-ASCII characters: R/ClassSangerAlignment.R R/ClassSangerContig.R R/ClassSangerRead.R Portable packages must use only ASCII characters in their R code and NAMESPACE directives, except perhaps in comments. Use \uxxxx escapes for other characters. Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII characters in files. * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘BiocStyle’ ‘knitr’ ‘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 QualityBasePlotly: no visible global function definition for ‘%>%’ SangerAlignment: no visible global function definition for ‘new’ SangerAlignmentServer: no visible global function definition for ‘%>%’ 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 global function definition for ‘%>%’ 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’ SetCharStyleList: no visible global function definition for ‘%>%’ 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’ checkTargetFastaName: no visible global function definition for ‘isEmpty’ 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,ObjectResults: 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 ‘new’ initialize,SangerAlignment: no visible global function definition for ‘callNextMethod’ initialize,SangerContig : : no visible global function definition for ‘new’ 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 ‘AAString’ 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: %>% AAString 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 code objects: ‘chromatogram_overwrite’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING S4 class codoc mismatches from Rd file 'ObjectResults-class.Rd': Slots for class 'ObjectResults' Code: creationResult errorMessages errorTypes printLevel readResultTable warningMessages warningTypes Docs: printLevel * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'SangerAlignment.Rd' ‘printLevel’ ‘processMethod’ Documented arguments not in \usage in Rd file 'SangerAlignment.Rd': ‘minFractionCallSA’ ‘maxFractionLostSA’ Undocumented arguments in Rd file 'SangerContig.Rd' ‘printLevel’ ‘processMethod’ Undocumented arguments in Rd file 'SangerRead.Rd' ‘printLevel’ 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 data for ASCII and uncompressed saves ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress sangerAlignmentData.RData 1.5Mb 698Kb xz sangerContigData.RData 451Kb 203Kb xz sangerReadFData.RData 269Kb 118Kb xz * 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 ... ERROR Running examples in ‘sangeranalyseR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: SangerAlignment-class > ### Title: SangerAlignment > ### Aliases: SangerAlignment-class > > ### ** Examples > > ## Simple example > rawDataDir <- system.file("extdata", package = "sangeranalyseR") > parentDir <- file.path(rawDataDir, 'Allolobophora_chlorotica', 'ACHLO') > my_aligned_contigs <- new("SangerAlignment", + ABIF_Directory = parentDir, + REGEX_SuffixForward = "_[0-9]*_F.ab1$", + REGEX_SuffixReverse = "_[0-9]*_R.ab1$") INFO [2024-12-11 04:16:38] ################################################# INFO [2024-12-11 04:16:38] #### Start creating SangerAlignment instance #### INFO [2024-12-11 04:16:38] ################################################# INFO [2024-12-11 04:16:38] >> You are using Regular Expression Method to group AB1 files! INFO [2024-12-11 04:16:38] ======================================================== INFO [2024-12-11 04:16:38] ================ Creating 'SangerContig' =============== INFO [2024-12-11 04:16:38] ======================================================== INFO [2024-12-11 04:16:38] >> Contig Name: 'Achl_ACHLO006-09' SUCCESS [2024-12-11 04:16:38] -------------------------------------------------------- SUCCESS [2024-12-11 04:16:38] -------- 'SangerRead' S4 instance is created !! -------- SUCCESS [2024-12-11 04:16:38] -------------------------------------------------------- SUCCESS [2024-12-11 04:16:38] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF). SUCCESS [2024-12-11 04:16:39] -------------------------------------------------------- SUCCESS [2024-12-11 04:16:39] -------- 'SangerRead' S4 instance is created !! -------- SUCCESS [2024-12-11 04:16:39] -------------------------------------------------------- SUCCESS [2024-12-11 04:16:39] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF). INFO [2024-12-11 04:16:39] >> The number of reads detected: 2 Error in DistanceMatrix(aln, correction = "Jukes-Cantor", penalizeGapLetterMatches = FALSE, : Invalid distance correction method. Calls: new ... initialize -> .local -> calculateContigSeq -> DistanceMatrix Execution halted * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 6 WARNINGs, 5 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/sangeranalyseR.Rcheck/00check.log’ for details.