Answers.Body: <p>Your code runs without error on my laptop (macOS 13.2.1; R v4.2.2; Rstudio 2022.07.2), so I have some further questions that might help with troubleshooting (too many to include in a comment):</p>
  <ul>
  <li>Does the <a href="https://github.com/roblanf/sangeranalyseR#quick-start-guide" rel="nofollow noreferrer">example from the docs</a> run without errors/warnings on your system?</li>
  <li>Did you install the sangeranalyseR package via Bioconductor (per the <a href="https://github.com/roblanf/sangeranalyseR#quick-start-guide" rel="nofollow noreferrer">docs</a>)?</li>
  <li>Do you have the most up-to-date Bioconducter installed?</li>
  <li>Have you tried running the example code in a 'fresh' session?</li>
  <li>Are you able to please run the command <code>sessionInfo()</code> and edit your question to include the output?</li>
  <li>If you run your example via the <a href="https://reprex.tidyverse.org/" rel="nofollow noreferrer">reprex package</a>, are there any differences between your output and my output?</li>
  </ul>
  <p>The code from your question run on my laptop:</p>
  <pre class="lang-r prettyprint-override"><code># BiocManager::install(&quot;sangeranalyseR&quot;)
  library(sangeranalyseR)
  #&gt; Loading required package: stringr
  #&gt; Loading required package: ape
  #&gt; Loading required package: Biostrings
  #&gt; Loading required package: BiocGenerics
  #&gt; 
  #&gt; Attaching package: 'BiocGenerics'
  #&gt; The following objects are masked from 'package:stats':
  #&gt; 
  #&gt;     IQR, mad, sd, var, xtabs
  #&gt; The following objects are masked from 'package:base':
  #&gt; 
  #&gt;     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
  #&gt;     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
  #&gt;     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
  #&gt;     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
  #&gt;     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
  #&gt;     table, tapply, union, unique, unsplit, which.max, which.min
  #&gt; Loading required package: S4Vectors
  #&gt; Loading required package: stats4
  #&gt; 
  #&gt; Attaching package: 'S4Vectors'
  #&gt; The following objects are masked from 'package:base':
  #&gt; 
  #&gt;     expand.grid, I, unname
  #&gt; Loading required package: IRanges
  #&gt; Loading required package: XVector
  #&gt; Loading required package: GenomeInfoDb
  #&gt; 
  #&gt; Attaching package: 'Biostrings'
  #&gt; The following object is masked from 'package:ape':
  #&gt; 
  #&gt;     complement
  #&gt; The following object is masked from 'package:base':
  #&gt; 
  #&gt;     strsplit
  #&gt; Loading required package: DECIPHER
  #&gt; Loading required package: RSQLite
  #&gt; Loading required package: parallel
  #&gt; Loading required package: reshape2
  #&gt; Loading required package: phangorn
  #&gt; Loading required package: sangerseqR
  #&gt; Loading required package: gridExtra
  #&gt; 
  #&gt; Attaching package: 'gridExtra'
  #&gt; The following object is masked from 'package:BiocGenerics':
  #&gt; 
  #&gt;     combine
  #&gt; Loading required package: shiny
  #&gt; Loading required package: shinydashboard
  #&gt; 
  #&gt; Attaching package: 'shinydashboard'
  #&gt; The following object is masked from 'package:graphics':
  #&gt; 
  #&gt;     box
  #&gt; Loading required package: shinyjs
  #&gt; 
  #&gt; Attaching package: 'shinyjs'
  #&gt; The following object is masked from 'package:shiny':
  #&gt; 
  #&gt;     runExample
  #&gt; The following object is masked from 'package:RSQLite':
  #&gt; 
  #&gt;     show
  #&gt; The following object is masked from 'package:Biostrings':
  #&gt; 
  #&gt;     show
  #&gt; The following object is masked from 'package:GenomeInfoDb':
  #&gt; 
  #&gt;     show
  #&gt; The following object is masked from 'package:XVector':
  #&gt; 
  #&gt;     show
  #&gt; The following object is masked from 'package:IRanges':
  #&gt; 
  #&gt;     show
  #&gt; The following object is masked from 'package:S4Vectors':
  #&gt; 
  #&gt;     show
  #&gt; The following object is masked from 'package:stats4':
  #&gt; 
  #&gt;     show
  #&gt; The following objects are masked from 'package:methods':
  #&gt; 
  #&gt;     removeClass, show
  #&gt; Loading required package: data.table
  #&gt; 
  #&gt; Attaching package: 'data.table'
  #&gt; The following objects are masked from 'package:reshape2':
  #&gt; 
  #&gt;     dcast, melt
  #&gt; The following object is masked from 'package:IRanges':
  #&gt; 
  #&gt;     shift
  #&gt; The following objects are masked from 'package:S4Vectors':
  #&gt; 
  #&gt;     first, second
  #&gt; Loading required package: plotly
  #&gt; Loading required package: ggplot2
  #&gt; 
  #&gt; Attaching package: 'plotly'
  #&gt; The following object is masked from 'package:ggplot2':
  #&gt; 
  #&gt;     last_plot
  #&gt; The following object is masked from 'package:phangorn':
  #&gt; 
  #&gt;     add_boxplot
  #&gt; The following object is masked from 'package:XVector':
  #&gt; 
  #&gt;     slice
  #&gt; The following object is masked from 'package:IRanges':
  #&gt; 
  #&gt;     slice
  #&gt; The following object is masked from 'package:S4Vectors':
  #&gt; 
  #&gt;     rename
  #&gt; The following object is masked from 'package:stats':
  #&gt; 
  #&gt;     filter
  #&gt; The following object is masked from 'package:graphics':
  #&gt; 
  #&gt;     layout
  #&gt; Loading required package: DT
  #&gt; 
  #&gt; Attaching package: 'DT'
  #&gt; The following objects are masked from 'package:shiny':
  #&gt; 
  #&gt;     dataTableOutput, renderDataTable
  #&gt; Loading required package: zeallot
  #&gt; Loading required package: excelR
  #&gt; Loading required package: shinycssloaders
  #&gt; Loading required package: ggdendro
  #&gt; Loading required package: shinyWidgets
  #&gt; 
  #&gt; Attaching package: 'shinyWidgets'
  #&gt; The following object is masked from 'package:shinyjs':
  #&gt; 
  #&gt;     alert
  #&gt; Loading required package: openxlsx
  #&gt; Loading required package: tools
  #&gt; Loading required package: rmarkdown
  #&gt; Loading required package: knitr
  #&gt; Loading required package: seqinr
  #&gt; 
  #&gt; Attaching package: 'seqinr'
  #&gt; The following object is masked from 'package:shiny':
  #&gt; 
  #&gt;     a
  #&gt; The following object is masked from 'package:sangerseqR':
  #&gt; 
  #&gt;     read.abif
  #&gt; The following object is masked from 'package:Biostrings':
  #&gt; 
  #&gt;     translate
  #&gt; The following objects are masked from 'package:ape':
  #&gt; 
  #&gt;     as.alignment, consensus
  #&gt; Loading required package: BiocStyle
  #&gt; 
  #&gt; Attaching package: 'BiocStyle'
  #&gt; The following objects are masked from 'package:rmarkdown':
  #&gt; 
  #&gt;     html_document, md_document, pdf_document
  #&gt; The following object is masked from 'package:shiny':
  #&gt; 
  #&gt;     markdown
  #&gt; Loading required package: logger
  #&gt; Welcome to sangeranalyseR
  data(&quot;sangerAlignmentData&quot;)
  data(&quot;sangerContigData&quot;)
  data(&quot;sangerReadFData&quot;)
  
  rawDataDir &lt;- system.file(&quot;extdata&quot;, package = &quot;sangeranalyseR&quot;)
  fastaFN &lt;- file.path(rawDataDir, &quot;fasta&quot;, &quot;SangerAlignment&quot;, &quot;Sanger_all_reads.fa&quot;)
  my_sangerAlignmentFa &lt;- new(&quot;SangerAlignment&quot;,
                              inputSource          = &quot;FASTA&quot;,
                              processMethod        = &quot;REGEX&quot;,
                              FASTA_File           = fastaFN,
                              REGEX_SuffixForward  = &quot;_[0-9]*_F<span class="math-container">$",
                          REGEX_SuffixReverse  = "_[0-9]*_R$</span>&quot;,
                              refAminoAcidSeq      = &quot;SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN&quot;,
                              minReadsNum           = 2,
                              minReadLength         = 20,
                              minFractionCall       = 0.5,
                              maxFractionLost       = 0.5,
                              geneticCode           = GENETIC_CODE,
                              acceptStopCodons      = TRUE,
                              readingFrame          = 1,
                              processorsNum         = 2)
  #&gt; Assessing frameshifts in nucleotide sequences:
  #&gt; ================================================================================
  #&gt; 
  #&gt; Time difference of 0.05 secs
  #&gt; Assessing frameshifts in nucleotide sequences:
  #&gt; ================================================================================
  #&gt; 
  #&gt; Time difference of 0.03 secs
  #&gt; Assessing frameshifts in nucleotide sequences:
  #&gt; ================================================================================
  #&gt; 
  #&gt; Time difference of 0.03 secs
  #&gt; Assessing frameshifts in nucleotide sequences:
  #&gt; ================================================================================
  #&gt; 
  #&gt; Time difference of 0.03 secs
  
  writeFasta(my_sangerAlignmentFa,
             outputDir         = tempdir(),
             compress          = FALSE,
             compression_level = NA,
             selection         = &quot;all&quot;)
  
  generateReport(my_sangerAlignmentFa,
                 outputDir           = tempdir(),
                 includeSangerRead   = TRUE,
                 includeSangerContig = TRUE)
  #&gt; processing file: SangerRead_Report_fasta.Rmd
  #&gt; output file: SangerRead_Report_fasta.knit.md
  #&gt; /usr/local/bin/pandoc +RTS -K512m -RTS SangerRead_Report_fasta.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /private/var/folders/gf/3p_ynkts411bs238rtw3y0b40000gn/T/Rtmplj2Uy8/SangerAlignment/Achl_ACHLO006-09/Sanger_all_reads/SangerRead_Report_fasta.html --lua-filter /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/gf/3p_ynkts411bs238rtw3y0b40000gn/T//Rtmplj2Uy8/rmarkdown-str3926187706b9.html
  #&gt; 
  #&gt; Output created: /private/var/folders/gf/3p_ynkts411bs238rtw3y0b40000gn/T/RtmplI8nQX/SangerAlignment/SangerAlignment_Report.html
  #&gt; [1] &quot;/private/var/folders/gf/3p_ynkts411bs238rtw3y0b40000gn/T/RtmplI8nQX/SangerAlignment/SangerAlignment_Report.html&quot;
  </code></pre>
  <p><sup>Created on 2023-03-02 with <a href="https://reprex.tidyverse.org" rel="nofollow noreferrer">reprex v2.0.2</a></sup></p>
  <hr />
  <p>Example from the docs:</p>
  <pre class="lang-r prettyprint-override"><code>library(sangeranalyseR)
  #&gt; Loading required package: stringr
  #&gt; Loading required package: ape
  #&gt; Loading required package: Biostrings
  #&gt; Loading required package: BiocGenerics
  #&gt; 
  #&gt; Attaching package: 'BiocGenerics'
  #&gt; The following objects are masked from 'package:stats':
  #&gt; 
  #&gt;     IQR, mad, sd, var, xtabs
  #&gt; The following objects are masked from 'package:base':
  #&gt; 
  #&gt;     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
  #&gt;     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
  #&gt;     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
  #&gt;     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
  #&gt;     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
  #&gt;     table, tapply, union, unique, unsplit, which.max, which.min
  #&gt; Loading required package: S4Vectors
  #&gt; Loading required package: stats4
  #&gt; 
  #&gt; Attaching package: 'S4Vectors'
  #&gt; The following objects are masked from 'package:base':
  #&gt; 
  #&gt;     expand.grid, I, unname
  #&gt; Loading required package: IRanges
  #&gt; Loading required package: XVector
  #&gt; Loading required package: GenomeInfoDb
  #&gt; 
  #&gt; Attaching package: 'Biostrings'
  #&gt; The following object is masked from 'package:ape':
  #&gt; 
  #&gt;     complement
  #&gt; The following object is masked from 'package:base':
  #&gt; 
  #&gt;     strsplit
  #&gt; Loading required package: DECIPHER
  #&gt; Loading required package: RSQLite
  #&gt; Loading required package: parallel
  #&gt; Loading required package: reshape2
  #&gt; Loading required package: phangorn
  #&gt; Loading required package: sangerseqR
  #&gt; Loading required package: gridExtra
  #&gt; 
  #&gt; Attaching package: 'gridExtra'
  #&gt; The following object is masked from 'package:BiocGenerics':
  #&gt; 
  #&gt;     combine
  #&gt; Loading required package: shiny
  #&gt; Loading required package: shinydashboard
  #&gt; 
  #&gt; Attaching package: 'shinydashboard'
  #&gt; The following object is masked from 'package:graphics':
  #&gt; 
  #&gt;     box
  #&gt; Loading required package: shinyjs
  #&gt; 
  #&gt; Attaching package: 'shinyjs'
  #&gt; The following object is masked from 'package:shiny':
  #&gt; 
  #&gt;     runExample
  #&gt; The following object is masked from 'package:RSQLite':
  #&gt; 
  #&gt;     show
  #&gt; The following object is masked from 'package:Biostrings':
  #&gt; 
  #&gt;     show
  #&gt; The following object is masked from 'package:GenomeInfoDb':
  #&gt; 
  #&gt;     show
  #&gt; The following object is masked from 'package:XVector':
  #&gt; 
  #&gt;     show
  #&gt; The following object is masked from 'package:IRanges':
  #&gt; 
  #&gt;     show
  #&gt; The following object is masked from 'package:S4Vectors':
  #&gt; 
  #&gt;     show
  #&gt; The following object is masked from 'package:stats4':
  #&gt; 
  #&gt;     show
  #&gt; The following objects are masked from 'package:methods':
  #&gt; 
  #&gt;     removeClass, show
  #&gt; Loading required package: data.table
  #&gt; 
  #&gt; Attaching package: 'data.table'
  #&gt; The following objects are masked from 'package:reshape2':
  #&gt; 
  #&gt;     dcast, melt
  #&gt; The following object is masked from 'package:IRanges':
  #&gt; 
  #&gt;     shift
  #&gt; The following objects are masked from 'package:S4Vectors':
  #&gt; 
  #&gt;     first, second
  #&gt; Loading required package: plotly
  #&gt; Loading required package: ggplot2
  #&gt; 
  #&gt; Attaching package: 'plotly'
  #&gt; The following object is masked from 'package:ggplot2':
  #&gt; 
  #&gt;     last_plot
  #&gt; The following object is masked from 'package:phangorn':
  #&gt; 
  #&gt;     add_boxplot
  #&gt; The following object is masked from 'package:XVector':
  #&gt; 
  #&gt;     slice
  #&gt; The following object is masked from 'package:IRanges':
  #&gt; 
  #&gt;     slice
  #&gt; The following object is masked from 'package:S4Vectors':
  #&gt; 
  #&gt;     rename
  #&gt; The following object is masked from 'package:stats':
  #&gt; 
  #&gt;     filter
  #&gt; The following object is masked from 'package:graphics':
  #&gt; 
  #&gt;     layout
  #&gt; Loading required package: DT
  #&gt; 
  #&gt; Attaching package: 'DT'
  #&gt; The following objects are masked from 'package:shiny':
  #&gt; 
  #&gt;     dataTableOutput, renderDataTable
  #&gt; Loading required package: zeallot
  #&gt; Loading required package: excelR
  #&gt; Loading required package: shinycssloaders
  #&gt; Loading required package: ggdendro
  #&gt; Loading required package: shinyWidgets
  #&gt; 
  #&gt; Attaching package: 'shinyWidgets'
  #&gt; The following object is masked from 'package:shinyjs':
  #&gt; 
  #&gt;     alert
  #&gt; Loading required package: openxlsx
  #&gt; Loading required package: tools
  #&gt; Loading required package: rmarkdown
  #&gt; Loading required package: knitr
  #&gt; Loading required package: seqinr
  #&gt; 
  #&gt; Attaching package: 'seqinr'
  #&gt; The following object is masked from 'package:shiny':
  #&gt; 
  #&gt;     a
  #&gt; The following object is masked from 'package:sangerseqR':
  #&gt; 
  #&gt;     read.abif
  #&gt; The following object is masked from 'package:Biostrings':
  #&gt; 
  #&gt;     translate
  #&gt; The following objects are masked from 'package:ape':
  #&gt; 
  #&gt;     as.alignment, consensus
  #&gt; Loading required package: BiocStyle
  #&gt; 
  #&gt; Attaching package: 'BiocStyle'
  #&gt; The following objects are masked from 'package:rmarkdown':
  #&gt; 
  #&gt;     html_document, md_document, pdf_document
  #&gt; The following object is masked from 'package:shiny':
  #&gt; 
  #&gt;     markdown
  #&gt; Loading required package: logger
  #&gt; Welcome to sangeranalyseR
  rawDataDir &lt;- system.file(&quot;extdata&quot;, package = &quot;sangeranalyseR&quot;)
  parentDir &lt;- file.path(rawDataDir, 'Allolobophora_chlorotica', 'ACHLO')
  
  ACHLO_contigs &lt;- SangerAlignment(ABIF_Directory     = parentDir,
                                   REGEX_SuffixForward = &quot;_[0-9]*_F.ab1<span class="math-container">$",
                               REGEX_SuffixReverse = "_[0-9]*_R.ab1$</span>&quot;)
  
  launchApp(ACHLO_contigs)
  writeFasta(ACHLO_contigs)
  generateReport(ACHLO_contigs)
  </code></pre>
  <p><sup>Created on 2023-03-02 with <a href="https://reprex.tidyverse.org" rel="nofollow noreferrer">reprex v2.0.2</a></sup></p>
  <hr />
  <p>My sessionInfo output:</p>
  <pre class="lang-r prettyprint-override"><code>sessionInfo()
  #&gt; R version 4.2.2 (2022-10-31)
  #&gt; Platform: x86_64-apple-darwin17.0 (64-bit)
  #&gt; Running under: macOS Big Sur ... 10.16
  #&gt; 
  #&gt; Matrix products: default
  #&gt; BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
  #&gt; LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
  #&gt; 
  #&gt; locale:
  #&gt; [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
  #&gt; 
  #&gt; attached base packages:
  #&gt;  [1] tools     parallel  stats4    stats     graphics  grDevices utils    
  #&gt;  [8] datasets  methods   base     
  #&gt; 
  #&gt; other attached packages:
  #&gt;  [1] sangeranalyseR_1.8.0  logger_0.2.2          BiocStyle_2.26.0     
  #&gt;  [4] seqinr_4.2-23         knitr_1.42            rmarkdown_2.20       
  #&gt;  [7] openxlsx_4.2.5.2      shinyWidgets_0.7.6    ggdendro_0.1.23      
  #&gt; [10] shinycssloaders_1.0.0 excelR_0.4.0          zeallot_0.1.0        
  #&gt; [13] DT_0.27               plotly_4.10.1         ggplot2_3.4.1        
  #&gt; [16] data.table_1.14.8     shinyjs_2.1.0         shinydashboard_0.7.2 
  #&gt; [19] shiny_1.7.4           gridExtra_2.3         sangerseqR_1.34.0    
  #&gt; [22] phangorn_2.11.1       reshape2_1.4.4        DECIPHER_2.26.0      
  #&gt; [25] RSQLite_2.3.0         Biostrings_2.66.0     GenomeInfoDb_1.34.9  
  #&gt; [28] XVector_0.38.0        IRanges_2.32.0        S4Vectors_0.36.2     
  #&gt; [31] BiocGenerics_0.44.0   ape_5.7               stringr_1.5.0        
  #&gt; 
  #&gt; loaded via a namespace (and not attached):
  #&gt;  [1] nlme_3.1-162           bitops_1.0-7           fs_1.6.1              
  #&gt;  [4] bit64_4.0.5            httr_1.4.5             R.cache_0.16.0        
  #&gt;  [7] bslib_0.4.2            utf8_1.2.3             R6_2.5.1              
  #&gt; [10] DBI_1.1.3              lazyeval_0.2.2         colorspace_2.1-0      
  #&gt; [13] ade4_1.7-22            withr_2.5.0            tidyselect_1.2.0      
  #&gt; [16] bit_4.0.5              compiler_4.2.2         cli_3.6.0             
  #&gt; [19] sass_0.4.5             scales_1.2.1           quadprog_1.5-8        
  #&gt; [22] digest_0.6.31          R.utils_2.12.2         pkgconfig_2.0.3       
  #&gt; [25] htmltools_0.5.4        styler_1.9.0           fastmap_1.1.1         
  #&gt; [28] htmlwidgets_1.6.1      rlang_1.0.6            rstudioapi_0.14       
  #&gt; [31] jquerylib_0.1.4        generics_0.1.3         jsonlite_1.8.4        
  #&gt; [34] zip_2.2.2              dplyr_1.1.0            R.oo_1.25.0           
  #&gt; [37] RCurl_1.98-1.10        magrittr_2.0.3         GenomeInfoDbData_1.2.9
  #&gt; [40] Matrix_1.5-3           Rcpp_1.0.10            munsell_0.5.0         
  #&gt; [43] fansi_1.0.4            lifecycle_1.0.3        R.methodsS3_1.8.2     
  #&gt; [46] stringi_1.7.12         yaml_2.3.7             MASS_7.3-58.2         
  #&gt; [49] zlibbioc_1.44.0        plyr_1.8.8             grid_4.2.2            
  #&gt; [52] blob_1.2.3             promises_1.2.0.1       crayon_1.5.2          
  #&gt; [55] lattice_0.20-45        pillar_1.8.1           igraph_1.4.1          
  #&gt; [58] codetools_0.2-19       fastmatch_1.1-3        reprex_2.0.2          
  #&gt; [61] glue_1.6.2             evaluate_0.20          BiocManager_1.30.20   
  #&gt; [64] vctrs_0.5.2            httpuv_1.6.9           gtable_0.3.1          
  #&gt; [67] purrr_1.0.1            tidyr_1.3.0            cachem_1.0.7          
  #&gt; [70] xfun_0.37              mime_0.12              xtable_1.8-4          
  #&gt; [73] later_1.3.0            viridisLite_0.4.1      tibble_3.1.8          
  #&gt; [76] memoise_2.0.1          ellipsis_0.3.2
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-03-03T07:48:24.370Z
Answers.Text: I used your code and ran the launchapp() function on the contigs. Below is the error code. Listening onhttp://127.0.0.1:6825
  Warning: Error in value[[3L]]: Couldn't normalize path in `addResourcePath`, with arguments: `prefix` = 'AdminLTE-2.0.6'; `directoryPath` = 'F:/biocbuild/bbs-3.16-bioc/R/library/shinydashboard/AdminLTE'
    3: runApp
    2: print.shiny.appobj
    1: <Anonymous>
Answers.UserDisplayName: Taeen Jidaan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-03-03T08:08:13.090Z
Answers.Text: Hi, Thank you for responding back. I am using Windows 10 R version 4.2.2. I edited my question to include the sessioninfo() for the package. I also recently commented the error I encountered from using your code. It's probably because my version of R is not updated because its Windows.
Answers.UserDisplayName: Taeen Jidaan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-03-03T08:08:23.457Z
Answers.Text: Another comment: I tried updating the Bioconductor package but I am using the newest version of it. However, when I used 'BiocManager::install(version='devel')', I ran across this error: Error: Bioconductor version '3.17' requires R version '4.3'; use
  `BiocManager::install(version = '3.16')` with R version 4.2; see
  https://bioconductor.org/install'. Is it because I am using Windows? If so, how could I use the example code in another program?
Answers.UserDisplayName: Taeen Jidaan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-03-03T08:11:06.347Z
Answers.Text: Another comment: I knitted your code again and this was the error I encountered: 
  `Error in parse_block(g[-1], g[1], params.src, markdown_mode) : 
  Duplicate chunk label 'unnamed-chunk-1', which has been used for the chunk:
  library(reprex)
  library(sangeranalyseR)
  data("sangerAlignmentData")
  data("sangerContigData")
  data("sangerReadFData")
  Calls: <Anonymous> ... process_file -> split_file -> lapply -> FUN -> parse_block                                                                           
  Execution halted'
Answers.UserDisplayName: Taeen Jidaan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-03-05T22:37:28.873Z
Answers.Text: Looks like you my have a few issues to deal with. One potential issue is your shiny package install. First thing I'd do is, in a new session, reinstall shiny (`install.packages("shiny")`) and run the example code from https://shiny.rstudio.com/gallery/plot-interaction-basic.html, then any issues with shiny and related packages should be able to be identified and solved.
Answers.UserDisplayName: jared_mamrot
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-03-02T04:13:57.590Z
Answers.LastActivityDate: 2023-03-03T04:34:48.757Z
Answers.LastEditDate: 2023-03-03T04:34:48.757Z
Answers.UserDisplayName: jared_mamrot
Body: <p>I am doing a project where I am reproducing the analysis from the article &quot;sangeranalyseR: Simple and Interactive Processing of Sanger Sequencing Data in R&quot;. Below is the example chunk for Sanger Alignment. Below are the package and datasets.</p>
  <pre class="lang-r prettyprint-override"><code>library(sangeranalyseR)
  data(&quot;sangerAlignmentData&quot;)
  data(&quot;sangerContigData&quot;)
  data(&quot;sangerReadFData&quot;)
  </code></pre>
  <p>Below is the code for Sanger Alignment, similar to the code for Sanger Contig and Sanger Reading.</p>
  <pre class="lang-r prettyprint-override"><code>rawDataDir &lt;- system.file(&quot;extdata&quot;, package = &quot;sangeranalyseR&quot;)
  fastaFN &lt;- file.path(rawDataDir, &quot;fasta&quot;, &quot;SangerAlignment&quot;, &quot;Sanger_all_reads.fa&quot;)
  my_sangerAlignmentFa &lt;- new(&quot;SangerAlignment&quot;,
                              inputSource          = &quot;FASTA&quot;,
                              processMethod        = &quot;REGEX&quot;,
                              FASTA_File           = fastaFN,
                              REGEX_SuffixForward  = &quot;_[0-9]*_F<span class="math-container">$",
                          REGEX_SuffixReverse  = "_[0-9]*_R$</span>&quot;,
                              refAminoAcidSeq      = &quot;SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN&quot;,
                              minReadsNum           = 2,
                              minReadLength         = 20,
                              minFractionCall       = 0.5,
                              maxFractionLost       = 0.5,
                              geneticCode           = GENETIC_CODE,
                              acceptStopCodons      = TRUE,
                              readingFrame          = 1,
                              processorsNum         = 1)
  
  launchApp(my_sangerAlignmentFa)
  
  writeFasta(my_sangerAlignmentFa,
             outputDir         = tempdir(),
             compress          = FALSE,
             compression_level = NA,
             selection         = &quot;all&quot;)
  
  generateReport(my_sangerAlignmentFa,
                 outputDir           = tempdir(),
                 includeSangerRead   = TRUE,
                 includeSangerContig = TRUE)
  </code></pre>
  <p>There are two problems that occurred for me. One is that the launchapp() function created an error for me stating</p>
  <pre><code>INFO [2023-03-01 14:25:52] Your input is 'SangerAlignment' S4 instance
  INFO [2023-03-01 14:25:52] SangerAlignment with 'FASTA' inputSource
  cannot run Shiny app (You don't need to do trimming or base calling)
  NULL
  </code></pre>
  <p>How can I fix this error?</p>
  <p>Another error that occurred within knitting. I ran the same code without the launchapp() function and an error that I never seen before said this</p>
  <pre><code>Quitting from lines NA-219 (SangerRead_Report_fasta.Rmd)  Error in parse_block(g[-1], g[1], params.src, markdown_mode) : 
  Duplicate chunk label 'unnamed-chunk-1', which has been used for the chunk:
  library(sangeranalyseR) library(rentrez) Calls: &lt;Anonymous&gt; ...
  process_file -&gt; split_file -&gt; lapply -&gt; FUN -&gt; parse_block
  
  Execution halted
  </code></pre>
  <p>Is it my RStudio or is the code itself. Is there anything I am missing?</p>
  <pre><code>sessionInfo(sangeranalysesR)
  R version 4.2.2 (2022-10-31 ucrt)
  Platform: x86_64-w64-mingw32/x64 (64-bit)
  Running under: Windows 10 x64 (build 22621)
  
  Matrix products: default
  
  locale:
  [1] LC_COLLATE=English_United States.utf8 
  [2] LC_CTYPE=English_United States.utf8   
  [3] LC_MONETARY=English_United States.utf8
  [4] LC_NUMERIC=C                          
  [5] LC_TIME=English_United States.utf8    
  
  attached base packages:
  character(0)
  
  other attached packages:
  [1] sangeranalyseR_1.8.0
  
  loaded via a namespace (and not attached):
    [1] utils_4.2.2            nlme_3.1-161          
    [3] fs_1.6.1               bitops_1.0-7          
    [5] bit64_4.0.5            httr_1.4.4            
    [7] GenomeInfoDb_1.34.6    tools_4.2.2           
    [9] bslib_0.4.2            utf8_1.2.2            
   [11] R6_2.5.1               DT_0.27               
   [13] DBI_1.1.3              lazyeval_0.2.2        
   [15] BiocGenerics_0.44.0    colorspace_2.1-0      
   [17] rhdf5filters_1.10.0    ade4_1.7-20           
   [19] withr_2.5.0            tidyselect_1.2.0      
   [21] gridExtra_2.3          phangorn_2.11.1       
   [23] bit_4.0.5              compiler_4.2.2        
   [25] cli_3.5.0              datasets_4.2.2        
   [27] shinyjs_2.1.0          plotly_4.10.1         
   [29] ggdendro_0.1.23        base_4.2.2            
   [31] sass_0.4.5             scales_1.2.1          
   [33] quadprog_1.5-8         stringr_1.5.0         
   [35] digest_0.6.31          rmarkdown_2.20        
   [37] sangerseqR_1.34.0      XVector_0.38.0        
   [39] pkgconfig_2.0.3        htmltools_0.5.4       
   [41] sessioninfo_1.2.2      fastmap_1.1.0         
   [43] excelR_0.4.0           grDevices_4.2.2       
   [45] htmlwidgets_1.6.1      rlang_1.0.6           
   [47] rstudioapi_0.14        RSQLite_2.2.20        
   [49] shiny_1.7.4            jquerylib_0.1.4       
   [51] generics_0.1.3         jsonlite_1.8.4        
   [53] BiocParallel_1.32.5    zip_2.2.2             
   [55] dplyr_1.1.0            RCurl_1.98-1.10       
   [57] magrittr_2.0.3         GenomeInfoDbData_1.2.9
   [59] biomformat_1.26.0      Matrix_1.5-3          
   [61] Rhdf5lib_1.20.0        Rcpp_1.0.10           
   [63] munsell_0.5.0          S4Vectors_0.36.1      
   [65] fansi_1.0.4            logger_0.2.2          
   [67] DECIPHER_2.26.0        ape_5.6-2             
   [69] shinycssloaders_1.0.0  lifecycle_1.0.3       
   [71] yaml_2.3.7             stringi_1.7.12        
   [73] MASS_7.3-58.2          zlibbioc_1.44.0       
   [75] rhdf5_2.42.0           plyr_1.8.8            
   [77] grid_4.2.2             blob_1.2.3            
   [79] parallel_4.2.2         promises_1.2.0.1      
   [81] shinydashboard_0.7.2   crayon_1.5.2          
   [83] methods_4.2.2          lattice_0.20-45       
   [85] Biostrings_2.66.0      zeallot_0.1.0         
   [87] knitr_1.42             pillar_1.8.1          
   [89] igraph_1.3.5           seqinr_4.2-23         
   [91] reshape2_1.4.4         codetools_0.2-19      
   [93] stats4_4.2.2           fastmatch_1.1-3       
   [95] reprex_2.0.2           BiocVersion_3.16.0    
   [97] glue_1.6.2             evaluate_0.20         
   [99] BiocManager_1.30.20    data.table_1.14.6     
  [101] vctrs_0.5.2            httpuv_1.6.8          
  [103] graphics_4.2.2         gtable_0.3.1          
  [105] purrr_1.0.1            tidyr_1.3.0           
  [107] cachem_1.0.6           ggplot2_3.4.0         
  [109] openxlsx_4.2.5.1       xfun_0.36             
  [111] mime_0.12              xtable_1.8-4          
  [113] later_1.3.0            viridisLite_0.4.1     
  [115] tibble_3.1.8           stats_4.2.2           
  [117] memoise_2.0.1          IRanges_2.32.0        
  [119] shinyWidgets_0.7.6     ellipsis_0.3.2        
  [121] BiocStyle_2.26.0
  <span class="math-container">```</span> 
  </code></pre>
  
Tags: <r><phylogenetics><bioconductor>
Title: Sanger Sequencing Knitting Error
ThreadText: # Sanger Sequencing Knitting Error
  
  (Asked by: username_0 on 2023-03-01)
  
  I am doing a project where I am reproducing the analysis from the article "sangeranalyseR: Simple and Interactive Processing of Sanger Sequencing Data in R". Below is the example chunk for Sanger Alignment. Below are the package and datasets.
  
  ```r
  library(sangeranalyseR)
  data("sangerAlignmentData")
  data("sangerContigData")
  data("sangerReadFData")
  
  ```
  
  Below is the code for Sanger Alignment, similar to the code for Sanger Contig and Sanger Reading.
  
  ```r
  rawDataDir <- system.file("extdata", package = "sangeranalyseR")
  fastaFN <- file.path(rawDataDir, "fasta", "SangerAlignment", "Sanger_all_reads.fa")
  my_sangerAlignmentFa <- new("SangerAlignment",
                              inputSource          = "FASTA",
                              processMethod        = "REGEX",
                              FASTA_File           = fastaFN,
                              REGEX_SuffixForward  = "_[0-9]*_F$",
                          REGEX_SuffixReverse  = "_[0-9]*_R$",
                              refAminoAcidSeq      = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN",
                              minReadsNum           = 2,
                              minReadLength         = 20,
                              minFractionCall       = 0.5,
                              maxFractionLost       = 0.5,
                              geneticCode           = GENETIC_CODE,
                              acceptStopCodons      = TRUE,
                              readingFrame          = 1,
                              processorsNum         = 1)
  
  launchApp(my_sangerAlignmentFa)
  
  writeFasta(my_sangerAlignmentFa,
             outputDir         = tempdir(),
             compress          = FALSE,
             compression_level = NA,
             selection         = "all")
  
  generateReport(my_sangerAlignmentFa,
                 outputDir           = tempdir(),
                 includeSangerRead   = TRUE,
                 includeSangerContig = TRUE)
  
  ```
  
  There are two problems that occurred for me. One is that the launchapp() function created an error for me stating
  
  ```
  INFO [2023-03-01 14:25:52] Your input is 'SangerAlignment' S4 instance
  INFO [2023-03-01 14:25:52] SangerAlignment with 'FASTA' inputSource
  cannot run Shiny app (You don't need to do trimming or base calling)
  NULL
  
  ```
  
  How can I fix this error?
  
  Another error that occurred within knitting. I ran the same code without the launchapp() function and an error that I never seen before said this
  
  ```
  Quitting from lines NA-219 (SangerRead_Report_fasta.Rmd)  Error in parse_block(g[-1], g[1], params.src, markdown_mode) : 
  Duplicate chunk label 'unnamed-chunk-1', which has been used for the chunk:
  library(sangeranalyseR) library(rentrez) Calls: <Anonymous> ...
  process_file -> split_file -> lapply -> FUN -> parse_block
  
  Execution halted
  
  ```
  
  Is it my RStudio or is the code itself. Is there anything I am missing?
  
  ```
  sessionInfo(sangeranalysesR)
  R version 4.2.2 (2022-10-31 ucrt)
  Platform: x86_64-w64-mingw32/x64 (64-bit)
  Running under: Windows 10 x64 (build 22621)
  
  Matrix products: default
  
  locale:
  [1] LC_COLLATE=English_United States.utf8 
  [2] LC_CTYPE=English_United States.utf8   
  [3] LC_MONETARY=English_United States.utf8
  [4] LC_NUMERIC=C                          
  [5] LC_TIME=English_United States.utf8    
  
  attached base packages:
  character(0)
  
  other attached packages:
  [1] sangeranalyseR_1.8.0
  
  loaded via a namespace (and not attached):
    [1] utils_4.2.2            nlme_3.1-161          
    [3] fs_1.6.1               bitops_1.0-7          
    [5] bit64_4.0.5            httr_1.4.4            
    [7] GenomeInfoDb_1.34.6    tools_4.2.2           
    [9] bslib_0.4.2            utf8_1.2.2            
   [11] R6_2.5.1               DT_0.27               
   [13] DBI_1.1.3              lazyeval_0.2.2        
   [15] BiocGenerics_0.44.0    colorspace_2.1-0      
   [17] rhdf5filters_1.10.0    ade4_1.7-20           
   [19] withr_2.5.0            tidyselect_1.2.0      
   [21] gridExtra_2.3          phangorn_2.11.1       
   [23] bit_4.0.5              compiler_4.2.2        
   [25] cli_3.5.0              datasets_4.2.2        
   [27] shinyjs_2.1.0          plotly_4.10.1         
   [29] ggdendro_0.1.23        base_4.2.2            
   [31] sass_0.4.5             scales_1.2.1          
   [33] quadprog_1.5-8         stringr_1.5.0         
   [35] digest_0.6.31          rmarkdown_2.20        
   [37] sangerseqR_1.34.0      XVector_0.38.0        
   [39] pkgconfig_2.0.3        htmltools_0.5.4       
   [41] sessioninfo_1.2.2      fastmap_1.1.0         
   [43] excelR_0.4.0           grDevices_4.2.2       
   [45] htmlwidgets_1.6.1      rlang_1.0.6           
   [47] rstudioapi_0.14        RSQLite_2.2.20        
   [49] shiny_1.7.4            jquerylib_0.1.4       
   [51] generics_0.1.3         jsonlite_1.8.4        
   [53] BiocParallel_1.32.5    zip_2.2.2             
   [55] dplyr_1.1.0            RCurl_1.98-1.10       
   [57] magrittr_2.0.3         GenomeInfoDbData_1.2.9
   [59] biomformat_1.26.0      Matrix_1.5-3          
   [61] Rhdf5lib_1.20.0        Rcpp_1.0.10           
   [63] munsell_0.5.0          S4Vectors_0.36.1      
   [65] fansi_1.0.4            logger_0.2.2          
   [67] DECIPHER_2.26.0        ape_5.6-2             
   [69] shinycssloaders_1.0.0  lifecycle_1.0.3       
   [71] yaml_2.3.7             stringi_1.7.12        
   [73] MASS_7.3-58.2          zlibbioc_1.44.0       
   [75] rhdf5_2.42.0           plyr_1.8.8            
   [77] grid_4.2.2             blob_1.2.3            
   [79] parallel_4.2.2         promises_1.2.0.1      
   [81] shinydashboard_0.7.2   crayon_1.5.2          
   [83] methods_4.2.2          lattice_0.20-45       
   [85] Biostrings_2.66.0      zeallot_0.1.0         
   [87] knitr_1.42             pillar_1.8.1          
   [89] igraph_1.3.5           seqinr_4.2-23         
   [91] reshape2_1.4.4         codetools_0.2-19      
   [93] stats4_4.2.2           fastmatch_1.1-3       
   [95] reprex_2.0.2           BiocVersion_3.16.0    
   [97] glue_1.6.2             evaluate_0.20         
   [99] BiocManager_1.30.20    data.table_1.14.6     
  [101] vctrs_0.5.2            httpuv_1.6.8          
  [103] graphics_4.2.2         gtable_0.3.1          
  [105] purrr_1.0.1            tidyr_1.3.0           
  [107] cachem_1.0.6           ggplot2_3.4.0         
  [109] openxlsx_4.2.5.1       xfun_0.36             
  [111] mime_0.12              xtable_1.8-4          
  [113] later_1.3.0            viridisLite_0.4.1     
  [115] tibble_3.1.8           stats_4.2.2           
  [117] memoise_2.0.1          IRanges_2.32.0        
  [119] shinyWidgets_0.7.6     ellipsis_0.3.2        
  [121] BiocStyle_2.26.0
  ``` 
  
  ```
  
  **Tags:** r, phylogenetics, bioconductor
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-03-02. Score: 3
  
  Your code runs without error on my laptop (macOS 13.2.1; R v4.2.2; Rstudio 2022.07.2), so I have some further questions that might help with troubleshooting (too many to include in a comment):
  
  * Does the [example from the docs](https://github.com/roblanf/sangeranalyseR#quick-start-guide) run without errors/warnings on your system?
  * Did you install the sangeranalyseR package via Bioconductor (per the [docs](https://github.com/roblanf/sangeranalyseR#quick-start-guide))?
  * Do you have the most up-to-date Bioconducter installed?
  * Have you tried running the example code in a 'fresh' session?
  * Are you able to please run the command `sessionInfo()` and edit your question to include the output?
  * If you run your example via the [reprex package](https://reprex.tidyverse.org/), are there any differences between your output and my output?
  
  The code from your question run on my laptop:
  
  ```r
  # BiocManager::install("sangeranalyseR")
  library(sangeranalyseR)
  #> Loading required package: stringr
  #> Loading required package: ape
  #> Loading required package: Biostrings
  #> Loading required package: BiocGenerics
  #> 
  #> Attaching package: 'BiocGenerics'
  #> The following objects are masked from 'package:stats':
  #> 
  #>     IQR, mad, sd, var, xtabs
  #> The following objects are masked from 'package:base':
  #> 
  #>     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
  #>     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
  #>     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
  #>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
  #>     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
  #>     table, tapply, union, unique, unsplit, which.max, which.min
  #> Loading required package: S4Vectors
  #> Loading required package: stats4
  #> 
  #> Attaching package: 'S4Vectors'
  #> The following objects are masked from 'package:base':
  #> 
  #>     expand.grid, I, unname
  #> Loading required package: IRanges
  #> Loading required package: XVector
  #> Loading required package: GenomeInfoDb
  #> 
  #> Attaching package: 'Biostrings'
  #> The following object is masked from 'package:ape':
  #> 
  #>     complement
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  #>     strsplit
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  #> Loading required package: sangerseqR
  #> Loading required package: gridExtra
  #> 
  #> Attaching package: 'gridExtra'
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  #> 
  #>     runExample
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  #> 
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  #> 
  #>     show
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  #> 
  #>     show
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  #> 
  #>     show
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  #> 
  #>     show
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  #> 
  #>     show
  #> The following objects are masked from 'package:methods':
  #> 
  #>     removeClass, show
  #> Loading required package: data.table
  #> 
  #> Attaching package: 'data.table'
  #> The following objects are masked from 'package:reshape2':
  #> 
  #>     dcast, melt
  #> The following object is masked from 'package:IRanges':
  #> 
  #>     shift
  #> The following objects are masked from 'package:S4Vectors':
  #> 
  #>     first, second
  #> Loading required package: plotly
  #> Loading required package: ggplot2
  #> 
  #> Attaching package: 'plotly'
  #> The following object is masked from 'package:ggplot2':
  #> 
  #>     last_plot
  #> The following object is masked from 'package:phangorn':
  #> 
  #>     add_boxplot
  #> The following object is masked from 'package:XVector':
  #> 
  #>     slice
  #> The following object is masked from 'package:IRanges':
  #> 
  #>     slice
  #> The following object is masked from 'package:S4Vectors':
  #> 
  #>     rename
  #> The following object is masked from 'package:stats':
  #> 
  #>     filter
  #> The following object is masked from 'package:graphics':
  #> 
  #>     layout
  #> Loading required package: DT
  #> 
  #> Attaching package: 'DT'
  #> The following objects are masked from 'package:shiny':
  #> 
  #>     dataTableOutput, renderDataTable
  #> Loading required package: zeallot
  #> Loading required package: excelR
  #> Loading required package: shinycssloaders
  #> Loading required package: ggdendro
  #> Loading required package: shinyWidgets
  #> 
  #> Attaching package: 'shinyWidgets'
  #> The following object is masked from 'package:shinyjs':
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  #>     alert
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  #> Loading required package: seqinr
  #> 
  #> Attaching package: 'seqinr'
  #> The following object is masked from 'package:shiny':
  #> 
  #>     a
  #> The following object is masked from 'package:sangerseqR':
  #> 
  #>     read.abif
  #> The following object is masked from 'package:Biostrings':
  #> 
  #>     translate
  #> The following objects are masked from 'package:ape':
  #> 
  #>     as.alignment, consensus
  #> Loading required package: BiocStyle
  #> 
  #> Attaching package: 'BiocStyle'
  #> The following objects are masked from 'package:rmarkdown':
  #> 
  #>     html_document, md_document, pdf_document
  #> The following object is masked from 'package:shiny':
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  #>     markdown
  #> Loading required package: logger
  #> Welcome to sangeranalyseR
  data("sangerAlignmentData")
  data("sangerContigData")
  data("sangerReadFData")
  
  rawDataDir <- system.file("extdata", package = "sangeranalyseR")
  fastaFN <- file.path(rawDataDir, "fasta", "SangerAlignment", "Sanger_all_reads.fa")
  my_sangerAlignmentFa <- new("SangerAlignment",
                              inputSource          = "FASTA",
                              processMethod        = "REGEX",
                              FASTA_File           = fastaFN,
                              REGEX_SuffixForward  = "_[0-9]*_F$",
                          REGEX_SuffixReverse  = "_[0-9]*_R$",
                              refAminoAcidSeq      = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN",
                              minReadsNum           = 2,
                              minReadLength         = 20,
                              minFractionCall       = 0.5,
                              maxFractionLost       = 0.5,
                              geneticCode           = GENETIC_CODE,
                              acceptStopCodons      = TRUE,
                              readingFrame          = 1,
                              processorsNum         = 2)
  #> Assessing frameshifts in nucleotide sequences:
  #> ================================================================================
  #> 
  #> Time difference of 0.05 secs
  #> Assessing frameshifts in nucleotide sequences:
  #> ================================================================================
  #> 
  #> Time difference of 0.03 secs
  #> Assessing frameshifts in nucleotide sequences:
  #> ================================================================================
  #> 
  #> Time difference of 0.03 secs
  #> Assessing frameshifts in nucleotide sequences:
  #> ================================================================================
  #> 
  #> Time difference of 0.03 secs
  
  writeFasta(my_sangerAlignmentFa,
             outputDir         = tempdir(),
             compress          = FALSE,
             compression_level = NA,
             selection         = "all")
  
  generateReport(my_sangerAlignmentFa,
                 outputDir           = tempdir(),
                 includeSangerRead   = TRUE,
                 includeSangerContig = TRUE)
  #> processing file: SangerRead_Report_fasta.Rmd
  #> output file: SangerRead_Report_fasta.knit.md
  #> /usr/local/bin/pandoc +RTS -K512m -RTS SangerRead_Report_fasta.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /private/var/folders/gf/3p_ynkts411bs238rtw3y0b40000gn/T/Rtmplj2Uy8/SangerAlignment/Achl_ACHLO006-09/Sanger_all_reads/SangerRead_Report_fasta.html --lua-filter /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/gf/3p_ynkts411bs238rtw3y0b40000gn/T//Rtmplj2Uy8/rmarkdown-str3926187706b9.html
  #> 
  #> Output created: /private/var/folders/gf/3p_ynkts411bs238rtw3y0b40000gn/T/RtmplI8nQX/SangerAlignment/SangerAlignment_Report.html
  #> [1] "/private/var/folders/gf/3p_ynkts411bs238rtw3y0b40000gn/T/RtmplI8nQX/SangerAlignment/SangerAlignment_Report.html"
  
  ```
  
  Created on 2023-03-02 with [reprex v2.0.2](https://reprex.tidyverse.org)
  
  ---
  
  Example from the docs:
  
  ```r
  library(sangeranalyseR)
  #> Loading required package: stringr
  #> Loading required package: ape
  #> Loading required package: Biostrings
  #> Loading required package: BiocGenerics
  #> 
  #> Attaching package: 'BiocGenerics'
  #> The following objects are masked from 'package:stats':
  #> 
  #>     IQR, mad, sd, var, xtabs
  #> The following objects are masked from 'package:base':
  #> 
  #>     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
  #>     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
  #>     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
  #>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
  #>     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
  #>     table, tapply, union, unique, unsplit, which.max, which.min
  #> Loading required package: S4Vectors
  #> Loading required package: stats4
  #> 
  #> Attaching package: 'S4Vectors'
  #> The following objects are masked from 'package:base':
  #> 
  #>     expand.grid, I, unname
  #> Loading required package: IRanges
  #> Loading required package: XVector
  #> Loading required package: GenomeInfoDb
  #> 
  #> Attaching package: 'Biostrings'
  #> The following object is masked from 'package:ape':
  #> 
  #>     complement
  #> The following object is masked from 'package:base':
  #> 
  #>     strsplit
  #> Loading required package: DECIPHER
  #> Loading required package: RSQLite
  #> Loading required package: parallel
  #> Loading required package: reshape2
  #> Loading required package: phangorn
  #> Loading required package: sangerseqR
  #> Loading required package: gridExtra
  #> 
  #> Attaching package: 'gridExtra'
  #> The following object is masked from 'package:BiocGenerics':
  #> 
  #>     combine
  #> Loading required package: shiny
  #> Loading required package: shinydashboard
  #> 
  #> Attaching package: 'shinydashboard'
  #> The following object is masked from 'package:graphics':
  #> 
  #>     box
  #> Loading required package: shinyjs
  #> 
  #> Attaching package: 'shinyjs'
  #> The following object is masked from 'package:shiny':
  #> 
  #>     runExample
  #> The following object is masked from 'package:RSQLite':
  #> 
  #>     show
  #> The following object is masked from 'package:Biostrings':
  #> 
  #>     show
  #> The following object is masked from 'package:GenomeInfoDb':
  #> 
  #>     show
  #> The following object is masked from 'package:XVector':
  #> 
  #>     show
  #> The following object is masked from 'package:IRanges':
  #> 
  #>     show
  #> The following object is masked from 'package:S4Vectors':
  #> 
  #>     show
  #> The following object is masked from 'package:stats4':
  #> 
  #>     show
  #> The following objects are masked from 'package:methods':
  #> 
  #>     removeClass, show
  #> Loading required package: data.table
  #> 
  #> Attaching package: 'data.table'
  #> The following objects are masked from 'package:reshape2':
  #> 
  #>     dcast, melt
  #> The following object is masked from 'package:IRanges':
  #> 
  #>     shift
  #> The following objects are masked from 'package:S4Vectors':
  #> 
  #>     first, second
  #> Loading required package: plotly
  #> Loading required package: ggplot2
  #> 
  #> Attaching package: 'plotly'
  #> The following object is masked from 'package:ggplot2':
  #> 
  #>     last_plot
  #> The following object is masked from 'package:phangorn':
  #> 
  #>     add_boxplot
  #> The following object is masked from 'package:XVector':
  #> 
  #>     slice
  #> The following object is masked from 'package:IRanges':
  #> 
  #>     slice
  #> The following object is masked from 'package:S4Vectors':
  #> 
  #>     rename
  #> The following object is masked from 'package:stats':
  #> 
  #>     filter
  #> The following object is masked from 'package:graphics':
  #> 
  #>     layout
  #> Loading required package: DT
  #> 
  #> Attaching package: 'DT'
  #> The following objects are masked from 'package:shiny':
  #> 
  #>     dataTableOutput, renderDataTable
  #> Loading required package: zeallot
  #> Loading required package: excelR
  #> Loading required package: shinycssloaders
  #> Loading required package: ggdendro
  #> Loading required package: shinyWidgets
  #> 
  #> Attaching package: 'shinyWidgets'
  #> The following object is masked from 'package:shinyjs':
  #> 
  #>     alert
  #> Loading required package: openxlsx
  #> Loading required package: tools
  #> Loading required package: rmarkdown
  #> Loading required package: knitr
  #> Loading required package: seqinr
  #> 
  #> Attaching package: 'seqinr'
  #> The following object is masked from 'package:shiny':
  #> 
  #>     a
  #> The following object is masked from 'package:sangerseqR':
  #> 
  #>     read.abif
  #> The following object is masked from 'package:Biostrings':
  #> 
  #>     translate
  #> The following objects are masked from 'package:ape':
  #> 
  #>     as.alignment, consensus
  #> Loading required package: BiocStyle
  #> 
  #> Attaching package: 'BiocStyle'
  #> The following objects are masked from 'package:rmarkdown':
  #> 
  #>     html_document, md_document, pdf_document
  #> The following object is masked from 'package:shiny':
  #> 
  #>     markdown
  #> Loading required package: logger
  #> Welcome to sangeranalyseR
  rawDataDir <- system.file("extdata", package = "sangeranalyseR")
  parentDir <- file.path(rawDataDir, 'Allolobophora_chlorotica', 'ACHLO')
  
  ACHLO_contigs <- SangerAlignment(ABIF_Directory     = parentDir,
                                   REGEX_SuffixForward = "_[0-9]*_F.ab1$",
                               REGEX_SuffixReverse = "_[0-9]*_R.ab1$")
  
  launchApp(ACHLO_contigs)
  writeFasta(ACHLO_contigs)
  generateReport(ACHLO_contigs)
  
  ```
  
  Created on 2023-03-02 with [reprex v2.0.2](https://reprex.tidyverse.org)
  
  ---
  
  My sessionInfo output:
  
  ```r
  sessionInfo()
  #> R version 4.2.2 (2022-10-31)
  #> Platform: x86_64-apple-darwin17.0 (64-bit)
  #> Running under: macOS Big Sur ... 10.16
  #> 
  #> Matrix products: default
  #> BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
  #> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
  #> 
  #> locale:
  #> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
  #> 
  #> attached base packages:
  #>  [1] tools     parallel  stats4    stats     graphics  grDevices utils    
  #>  [8] datasets  methods   base     
  #> 
  #> other attached packages:
  #>  [1] sangeranalyseR_1.8.0  logger_0.2.2          BiocStyle_2.26.0     
  #>  [4] seqinr_4.2-23         knitr_1.42            rmarkdown_2.20       
  #>  [7] openxlsx_4.2.5.2      shinyWidgets_0.7.6    ggdendro_0.1.23      
  #> [10] shinycssloaders_1.0.0 excelR_0.4.0          zeallot_0.1.0        
  #> [13] DT_0.27               plotly_4.10.1         ggplot2_3.4.1        
  #> [16] data.table_1.14.8     shinyjs_2.1.0         shinydashboard_0.7.2 
  #> [19] shiny_1.7.4           gridExtra_2.3         sangerseqR_1.34.0    
  #> [22] phangorn_2.11.1       reshape2_1.4.4        DECIPHER_2.26.0      
  #> [25] RSQLite_2.3.0         Biostrings_2.66.0     GenomeInfoDb_1.34.9  
  #> [28] XVector_0.38.0        IRanges_2.32.0        S4Vectors_0.36.2     
  #> [31] BiocGenerics_0.44.0   ape_5.7               stringr_1.5.0        
  #> 
  #> loaded via a namespace (and not attached):
  #>  [1] nlme_3.1-162           bitops_1.0-7           fs_1.6.1              
  #>  [4] bit64_4.0.5            httr_1.4.5             R.cache_0.16.0        
  #>  [7] bslib_0.4.2            utf8_1.2.3             R6_2.5.1              
  #> [10] DBI_1.1.3              lazyeval_0.2.2         colorspace_2.1-0      
  #> [13] ade4_1.7-22            withr_2.5.0            tidyselect_1.2.0      
  #> [16] bit_4.0.5              compiler_4.2.2         cli_3.6.0             
  #> [19] sass_0.4.5             scales_1.2.1           quadprog_1.5-8        
  #> [22] digest_0.6.31          R.utils_2.12.2         pkgconfig_2.0.3       
  #> [25] htmltools_0.5.4        styler_1.9.0           fastmap_1.1.1         
  #> [28] htmlwidgets_1.6.1      rlang_1.0.6            rstudioapi_0.14       
  #> [31] jquerylib_0.1.4        generics_0.1.3         jsonlite_1.8.4        
  #> [34] zip_2.2.2              dplyr_1.1.0            R.oo_1.25.0           
  #> [37] RCurl_1.98-1.10        magrittr_2.0.3         GenomeInfoDbData_1.2.9
  #> [40] Matrix_1.5-3           Rcpp_1.0.10            munsell_0.5.0         
  #> [43] fansi_1.0.4            lifecycle_1.0.3        R.methodsS3_1.8.2     
  #> [46] stringi_1.7.12         yaml_2.3.7             MASS_7.3-58.2         
  #> [49] zlibbioc_1.44.0        plyr_1.8.8             grid_4.2.2            
  #> [52] blob_1.2.3             promises_1.2.0.1       crayon_1.5.2          
  #> [55] lattice_0.20-45        pillar_1.8.1           igraph_1.4.1          
  #> [58] codetools_0.2-19       fastmatch_1.1-3        reprex_2.0.2          
  #> [61] glue_1.6.2             evaluate_0.20          BiocManager_1.30.20   
  #> [64] vctrs_0.5.2            httpuv_1.6.9           gtable_0.3.1          
  #> [67] purrr_1.0.1            tidyr_1.3.0            cachem_1.0.7          
  #> [70] xfun_0.37              mime_0.12              xtable_1.8-4          
  #> [73] later_1.3.0            viridisLite_0.4.1      tibble_3.1.8          
  #> [76] memoise_2.0.1          ellipsis_0.3.2
  
  ```
  
  > **Comments:**
  > **username_0**: I used your code and ran the launchapp() function on the contigs. Below is the error code. Listening onhttp://127.0.0.1:6825 Warning: Error in value[[3L]]: Couldn't normalize path in `addResourcePath`, with arguments: `prefix` = 'AdminLTE-2.0.6'; `directoryPath` = 'F:/biocbuild/bbs-3.16-bioc/R/library/shinydashboard/AdminLTE'   3: runApp   2: print.shiny.appobj   1: <Anonymous>  
  > **username_0**: Hi, Thank you for responding back. I am using Windows 10 R version 4.2.2. I edited my question to include the sessioninfo() for the package. I also recently commented the error I encountered from using your code. It's probably because my version of R is not updated because its Windows.  
  > **username_0**: Another comment: I tried updating the Bioconductor package but I am using the newest version of it. However, when I used 'BiocManager::install(version='devel')', I ran across this error: Error: Bioconductor version '3.17' requires R version '4.3'; use `BiocManager::install(version = '3.16')` with R version 4.2; see https://bioconductor.org/install'. Is it because I am using Windows? If so, how could I use the example code in another program?  
  > **username_0**: Another comment: I knitted your code again and this was the error I encountered:  `Error in parse_block(g[-1], g[1], params.src, markdown_mode) :  Duplicate chunk label 'unnamed-chunk-1', which has been used for the chunk: library(reprex) library(sangeranalyseR) data("sangerAlignmentData") data("sangerContigData") data("sangerReadFData") Calls: <Anonymous> ... process_file -> split_file -> lapply -> FUN -> parse_block                                                                            Execution halted'  
  > **username_1**: Looks like you my have a few issues to deal with. One potential issue is your shiny package install. First thing I'd do is, in a new session, reinstall shiny (`install.packages("shiny")`) and run the example code from https://shiny.rstudio.com/gallery/plot-interaction-basic.html, then any issues with shiny and related packages should be able to be identified and solved.  
  
  ---
  
  