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### Running command:
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###   /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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/sangeranalyseR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sangeranalyseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sangeranalyseR’ version ‘1.10.0’
* 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', '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 ... NOTE
  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 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘BiocStyle’ ‘knitr’ ‘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
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 : <anonymous>: 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 : <anonymous>: 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 documentation object 'ObjectResults-class':
Slots for class 'ObjectResults'
  Code: creationResult errorMessages errorTypes printLevel
        readResultTable warningMessages warningTypes
  Docs: printLevel

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'SangerAlignment'
  ‘printLevel’ ‘processMethod’
Documented arguments not in \usage in documentation object 'SangerAlignment':
  ‘minFractionCallSA’ ‘maxFractionLostSA’

Undocumented arguments in documentation object 'SangerContig'
  ‘printLevel’ ‘processMethod’

Undocumented arguments in documentation object 'SangerRead'
  ‘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 ... WARNING
  Failed with error:  'package 'phangorn' could not be loaded'
  Error loading dataset 'qualityReportData':
   Error in .requirePackage(package) : 
    unable to find required package 'sangeranalyseR'
  
  Failed with error:  'package 'phangorn' could not be loaded'
  Error loading dataset 'sangerAlignmentData':
   Error in .requirePackage(package) : 
    unable to find required package 'sangeranalyseR'
  
  Failed with error:  'package 'phangorn' could not be loaded'
  Error loading dataset 'sangerContigData':
   Error in .requirePackage(package) : 
    unable to find required package 'sangeranalyseR'
  
  Failed with error:  'package 'phangorn' could not be loaded'
  Error loading dataset 'sangerReadFData':
   Error in .requirePackage(package) : 
    unable to find required package 'sangeranalyseR'
  
  The dataset(s) may use package(s) not declared in Depends/Imports.
* 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    696Kb       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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
SangerAlignment-class 56.663  1.051  99.899
SangerAlignment       11.515  0.209  20.986
SangerContig-class    11.250  0.213  19.951
SangerRead-class       2.912  0.060   5.039
* 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: 7 WARNINGs, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/sangeranalyseR.Rcheck/00check.log’
for details.