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This page was generated on 2022-03-17 11:08:46 -0400 (Thu, 17 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4060
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for sangeranalyseR on riesling1


To the developers/maintainers of the sangeranalyseR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sangeranalyseR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1699/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sangeranalyseR 1.5.1  (landing page)
Kuan-Hao Chao
Snapshot Date: 2022-03-16 13:55:23 -0400 (Wed, 16 Mar 2022)
git_url: https://git.bioconductor.org/packages/sangeranalyseR
git_branch: master
git_last_commit: e892ca0
git_last_commit_date: 2022-01-11 20:47:45 -0400 (Tue, 11 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: sangeranalyseR
Version: 1.5.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sangeranalyseR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings sangeranalyseR_1.5.1.tar.gz
StartedAt: 2022-03-16 20:06:05 -0400 (Wed, 16 Mar 2022)
EndedAt: 2022-03-16 20:10:54 -0400 (Wed, 16 Mar 2022)
EllapsedTime: 289.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: sangeranalyseR.Rcheck
Warnings: 7

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sangeranalyseR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings sangeranalyseR_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/sangeranalyseR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sangeranalyseR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sangeranalyseR' version '1.5.1'
* 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 whether package 'sangeranalyseR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   5.4Mb
* 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' '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 the DESCRIPTION file.
* 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    695Kb       xz
  sangerContigData.RData       451Kb    204Kb       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 41.94   0.69   42.66
SangerContig-class     9.22   0.07    9.30
SangerAlignment        7.89   0.11    8.09
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/sangeranalyseR.Rcheck/00check.log'
for details.



Installation output

sangeranalyseR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL sangeranalyseR
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'sangeranalyseR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '==' 
** help
*** installing help indices
  converting help for package 'sangeranalyseR'
    finding HTML links ... done
    ChromatogramParam-class                 html  
    MakeBaseCalls-methods                   html  
    ObjectResults-class                     html  
    QualityReport-class-qualityBasePlot     html  
    QualityReport-class-updateQualityParam
                                            html  
    QualityReport-class                     html  
    SangerAlignment-class-generateReportSA
                                            html  
    SangerAlignment-class-launchAppSA       html  
    SangerAlignment-class-updateQualityParam
                                            html  
    SangerAlignment-class-writeFastaSA      html  
    SangerAlignment-class                   html  
    SangerAlignment                         html  
    SangerContig-class-generateReportSC     html  
    SangerContig-class-launchAppSC          html  
    SangerContig-class-readTable            html  
    SangerContig-class-updateQualityParam   html  
    SangerContig-class-writeFastaSC         html  
    SangerContig-class                      html  
    SangerContig                            html  
    SangerRead-class-MakeBaseCalls          html  
    SangerRead-class-generateReportSR       html  
    SangerRead-class-qualityBasePlot        html  
    SangerRead-class-readTable              html  
    SangerRead-class-updateQualityParam     html  
    SangerRead-class-writeFastaSR           html  
    SangerRead-class                        html  
    SangerRead                              html  
    generateReport                          html  
    generateReportSA-methods                html  
    generateReportSC-methods                html  
    generateReportSR-methods                html  
    launchApp                               html  
    launchAppSA-methods                     html  
    launchAppSC-methods                     html  
    qualityBasePlot-methods                 html  
    qualityReportData                       html  
    readTable-methods                       html  
    sangerAlignmentData                     html  
    sangerContigData                        html  
    sangerReadFData                         html  
    sangeranalyseR                          html  
    updateQualityParam-methods              html  
    writeFasta                              html  
    writeFastaSA-methods                    html  
    writeFastaSC-methods                    html  
    writeFastaSR-methods                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sangeranalyseR)
Making 'packages.html' ... done

Tests output

sangeranalyseR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> 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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, 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':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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: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
> 
> 
> test_check("sangeranalyseR")
INFO [2022-03-16 20:09:50] #################################################
INFO [2022-03-16 20:09:50] #### Start creating SangerAlignment instance ####
INFO [2022-03-16 20:09:50] #################################################
INFO [2022-03-16 20:09:51]   >> You are using Regular Expression Method to group AB1 files!
INFO [2022-03-16 20:09:51] ========================================================
INFO [2022-03-16 20:09:51] ================ Creating 'SangerContig' ===============
INFO [2022-03-16 20:09:51] ========================================================
INFO [2022-03-16 20:09:51]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2022-03-16 20:09:51] --------------------------------------------------------
SUCCESS [2022-03-16 20:09:51] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:09:51] --------------------------------------------------------
SUCCESS [2022-03-16 20:09:51]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2022-03-16 20:09:52] --------------------------------------------------------
SUCCESS [2022-03-16 20:09:52] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:09:52] --------------------------------------------------------
SUCCESS [2022-03-16 20:09:52]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2022-03-16 20:09:52]    >> The number of reads detected: 2
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
SUCCESS [2022-03-16 20:09:53] ==========================================================
SUCCESS [2022-03-16 20:09:53] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2022-03-16 20:09:53] ==========================================================
INFO [2022-03-16 20:09:53]    >> 2 read(s) created from ABIF file.
INFO [2022-03-16 20:09:53]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2022-03-16 20:09:53]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2022-03-16 20:09:53] ========================================================
INFO [2022-03-16 20:09:53] ================ Creating 'SangerContig' ===============
INFO [2022-03-16 20:09:53] ========================================================
INFO [2022-03-16 20:09:53]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2022-03-16 20:09:54] --------------------------------------------------------
SUCCESS [2022-03-16 20:09:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:09:54] --------------------------------------------------------
SUCCESS [2022-03-16 20:09:54]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2022-03-16 20:09:54] --------------------------------------------------------
SUCCESS [2022-03-16 20:09:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:09:54] --------------------------------------------------------
SUCCESS [2022-03-16 20:09:54]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2022-03-16 20:09:54]    >> The number of reads detected: 2
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
SUCCESS [2022-03-16 20:09:55] ==========================================================
SUCCESS [2022-03-16 20:09:55] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2022-03-16 20:09:55] ==========================================================
INFO [2022-03-16 20:09:55]    >> 2 read(s) created from ABIF file.
INFO [2022-03-16 20:09:55]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2022-03-16 20:09:55]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2022-03-16 20:09:55] ========================================================
INFO [2022-03-16 20:09:55] ================ Creating 'SangerContig' ===============
INFO [2022-03-16 20:09:55] ========================================================
INFO [2022-03-16 20:09:55]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2022-03-16 20:09:56] --------------------------------------------------------
SUCCESS [2022-03-16 20:09:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:09:56] --------------------------------------------------------
SUCCESS [2022-03-16 20:09:56]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2022-03-16 20:09:56] --------------------------------------------------------
SUCCESS [2022-03-16 20:09:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:09:56] --------------------------------------------------------
SUCCESS [2022-03-16 20:09:56]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2022-03-16 20:09:56]    >> The number of reads detected: 2
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
SUCCESS [2022-03-16 20:09:57] ==========================================================
SUCCESS [2022-03-16 20:09:57] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2022-03-16 20:09:58] ==========================================================
INFO [2022-03-16 20:09:58]    >> 2 read(s) created from ABIF file.
INFO [2022-03-16 20:09:58]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2022-03-16 20:09:58]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2022-03-16 20:09:58] ========================================================
INFO [2022-03-16 20:09:58] ================ Creating 'SangerContig' ===============
INFO [2022-03-16 20:09:58] ========================================================
INFO [2022-03-16 20:09:58]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2022-03-16 20:09:58] --------------------------------------------------------
SUCCESS [2022-03-16 20:09:58] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:09:58] --------------------------------------------------------
SUCCESS [2022-03-16 20:09:58]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2022-03-16 20:09:58] --------------------------------------------------------
SUCCESS [2022-03-16 20:09:58] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:09:58] --------------------------------------------------------
SUCCESS [2022-03-16 20:09:58]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2022-03-16 20:09:58]    >> The number of reads detected: 2
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
SUCCESS [2022-03-16 20:10:00] ==========================================================
SUCCESS [2022-03-16 20:10:00] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2022-03-16 20:10:00] ==========================================================
INFO [2022-03-16 20:10:00]    >> 2 read(s) created from ABIF file.
INFO [2022-03-16 20:10:00]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2022-03-16 20:10:00]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2022-03-16 20:10:00] Aligning consensus reads ... 
SUCCESS [2022-03-16 20:10:00] #############################################################
SUCCESS [2022-03-16 20:10:00] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2022-03-16 20:10:00] #############################################################
INFO [2022-03-16 20:10:00]   >> 4 contigs detected from 'regular expression'.
INFO [2022-03-16 20:10:00]       >> Contig 'Achl_ACHLO006-09':
INFO [2022-03-16 20:10:00]           >> 1 forward reads.
INFO [2022-03-16 20:10:00]           >> 1 reverse reads.
INFO [2022-03-16 20:10:00]       >> Contig 'Achl_ACHLO007-09':
INFO [2022-03-16 20:10:00]           >> 1 forward reads.
INFO [2022-03-16 20:10:00]           >> 1 reverse reads.
INFO [2022-03-16 20:10:00]       >> Contig 'Achl_ACHLO040-09':
INFO [2022-03-16 20:10:00]           >> 1 forward reads.
INFO [2022-03-16 20:10:00]           >> 1 reverse reads.
INFO [2022-03-16 20:10:00]       >> Contig 'Achl_ACHLO041-09':
INFO [2022-03-16 20:10:00]           >> 1 forward reads.
INFO [2022-03-16 20:10:00]           >> 1 reverse reads.
INFO [2022-03-16 20:10:00]   >> 8 reads created from ABIF file.
INFO [2022-03-16 20:10:00]   >> Reads are trimmed by 'M1 - Mott’s trimming algorithm'.
DEBUG [2022-03-16 20:10:00]    >> For more information, please run 'object'.
DEBUG [2022-03-16 20:10:00]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2022-03-16 20:10:01] #################################################
INFO [2022-03-16 20:10:01] #### Start creating SangerAlignment instance ####
INFO [2022-03-16 20:10:01] #################################################
INFO [2022-03-16 20:10:01] **** You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2022-03-16 20:10:01] ========================================================
INFO [2022-03-16 20:10:01] ================ Creating 'SangerContig' ===============
INFO [2022-03-16 20:10:01] ========================================================
INFO [2022-03-16 20:10:01]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2022-03-16 20:10:01] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:01] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:01]    >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2022-03-16 20:10:01] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:01] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:01]    >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2022-03-16 20:10:01]    >> The number of reads detected: 2
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
SUCCESS [2022-03-16 20:10:02] ==========================================================
SUCCESS [2022-03-16 20:10:02] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2022-03-16 20:10:02] ==========================================================
INFO [2022-03-16 20:10:02]    >> 2 read(s) created from FASTA file.
INFO [2022-03-16 20:10:02]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2022-03-16 20:10:02]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2022-03-16 20:10:02] ========================================================
INFO [2022-03-16 20:10:02] ================ Creating 'SangerContig' ===============
INFO [2022-03-16 20:10:02] ========================================================
INFO [2022-03-16 20:10:02]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2022-03-16 20:10:02] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:02] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:02] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:02]    >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2022-03-16 20:10:02] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:02] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:02] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:02]    >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2022-03-16 20:10:02]    >> The number of reads detected: 2
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
SUCCESS [2022-03-16 20:10:04] ==========================================================
SUCCESS [2022-03-16 20:10:04] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2022-03-16 20:10:04] ==========================================================
INFO [2022-03-16 20:10:04]    >> 2 read(s) created from FASTA file.
INFO [2022-03-16 20:10:04]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2022-03-16 20:10:04]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2022-03-16 20:10:04] ========================================================
INFO [2022-03-16 20:10:04] ================ Creating 'SangerContig' ===============
INFO [2022-03-16 20:10:04] ========================================================
INFO [2022-03-16 20:10:04]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2022-03-16 20:10:04] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:04] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:04]    >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2022-03-16 20:10:04] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:04] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:04]    >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2022-03-16 20:10:04]    >> The number of reads detected: 2
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
SUCCESS [2022-03-16 20:10:05] ==========================================================
SUCCESS [2022-03-16 20:10:05] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2022-03-16 20:10:05] ==========================================================
INFO [2022-03-16 20:10:05]    >> 2 read(s) created from FASTA file.
INFO [2022-03-16 20:10:05]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2022-03-16 20:10:05]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2022-03-16 20:10:05] ========================================================
INFO [2022-03-16 20:10:05] ================ Creating 'SangerContig' ===============
INFO [2022-03-16 20:10:05] ========================================================
INFO [2022-03-16 20:10:05]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2022-03-16 20:10:06] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:06] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:06]    >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2022-03-16 20:10:06] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:06] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:06]    >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2022-03-16 20:10:06]    >> The number of reads detected: 2
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
SUCCESS [2022-03-16 20:10:07] ==========================================================
SUCCESS [2022-03-16 20:10:07] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2022-03-16 20:10:07] ==========================================================
INFO [2022-03-16 20:10:07]    >> 2 read(s) created from FASTA file.
INFO [2022-03-16 20:10:07]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2022-03-16 20:10:07]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2022-03-16 20:10:07] Aligning consensus reads ... 
SUCCESS [2022-03-16 20:10:08] #############################################################
SUCCESS [2022-03-16 20:10:08] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2022-03-16 20:10:08] #############################################################
INFO [2022-03-16 20:10:08]   >> 4 contigs detected from 'regular expression'.
INFO [2022-03-16 20:10:08]       >> Contig 'Achl_ACHLO006-09':
INFO [2022-03-16 20:10:08]           >> 1 forward reads.
INFO [2022-03-16 20:10:08]           >> 1 reverse reads.
INFO [2022-03-16 20:10:08]       >> Contig 'Achl_ACHLO007-09':
INFO [2022-03-16 20:10:08]           >> 1 forward reads.
INFO [2022-03-16 20:10:08]           >> 1 reverse reads.
INFO [2022-03-16 20:10:08]       >> Contig 'Achl_ACHLO040-09':
INFO [2022-03-16 20:10:08]           >> 1 forward reads.
INFO [2022-03-16 20:10:08]           >> 1 reverse reads.
INFO [2022-03-16 20:10:08]       >> Contig 'Achl_ACHLO041-09':
INFO [2022-03-16 20:10:08]           >> 1 forward reads.
INFO [2022-03-16 20:10:08]           >> 1 reverse reads.
INFO [2022-03-16 20:10:08]   >> 8 reads created from FASTA file.
DEBUG [2022-03-16 20:10:08]    >> For more information, please run 'object'.
DEBUG [2022-03-16 20:10:08]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2022-03-16 20:10:08] ========================================================
INFO [2022-03-16 20:10:08] ================ Creating 'SangerContig' ===============
INFO [2022-03-16 20:10:08] ========================================================
INFO [2022-03-16 20:10:08]   >> Contig Name: 'Achl_ACHLO006-09'
INFO [2022-03-16 20:10:08]   >> You are using Regular Expression Method to group AB1 files!
INFO [2022-03-16 20:10:08] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2022-03-16 20:10:08] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:08] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:08] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:08]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2022-03-16 20:10:09] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:09] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:09] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:09]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2022-03-16 20:10:09]    >> The number of reads detected: 2
INFO [2022-03-16 20:10:09] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.02 secs
SUCCESS [2022-03-16 20:10:10] ==========================================================
SUCCESS [2022-03-16 20:10:10] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2022-03-16 20:10:10] ==========================================================
INFO [2022-03-16 20:10:10]    >> 2 read(s) created from ABIF file.
INFO [2022-03-16 20:10:10]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2022-03-16 20:10:10]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2022-03-16 20:10:10]    >> Trimmed by 'M1 - Mott’s trimming algorithm'.
DEBUG [2022-03-16 20:10:10]    >> For more information, please run 'object'
DEBUG [2022-03-16 20:10:10]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2022-03-16 20:10:10] ========================================================
INFO [2022-03-16 20:10:10] ================ Creating 'SangerContig' ===============
INFO [2022-03-16 20:10:10] ========================================================
INFO [2022-03-16 20:10:10]   >> Contig Name: 'Achl_RBNII384-13'
INFO [2022-03-16 20:10:10]   >> You are using Regular Expression Method to group AB1 files!
INFO [2022-03-16 20:10:10] >> Your contig name is Achl_RBNII384-13
SUCCESS [2022-03-16 20:10:10] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:10] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:10] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:10]    >> 'Achl_RBNII384-13_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2022-03-16 20:10:10] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:10] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:10] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:10]    >> 'Achl_RBNII384-13_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2022-03-16 20:10:10]    >> The number of reads detected: 2
INFO [2022-03-16 20:10:10] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
SUCCESS [2022-03-16 20:10:11] ==========================================================
SUCCESS [2022-03-16 20:10:11] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2022-03-16 20:10:11] ==========================================================
INFO [2022-03-16 20:10:11]    >> 2 read(s) created from ABIF file.
INFO [2022-03-16 20:10:11]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2022-03-16 20:10:11]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2022-03-16 20:10:11]    >> Trimmed by 'M1 - Mott’s trimming algorithm'.
DEBUG [2022-03-16 20:10:11]    >> For more information, please run 'object'
DEBUG [2022-03-16 20:10:11]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2022-03-16 20:10:11] ========================================================
INFO [2022-03-16 20:10:11] ================ Creating 'SangerContig' ===============
INFO [2022-03-16 20:10:11] ========================================================
INFO [2022-03-16 20:10:11]   >> Contig Name: 'Achl_ACHLO006-09'
INFO [2022-03-16 20:10:11]   >> You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2022-03-16 20:10:11] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2022-03-16 20:10:12] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:12] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:12] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:12]    >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2022-03-16 20:10:12] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:12] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:12] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:12]    >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2022-03-16 20:10:12]    >> The number of reads detected: 2
INFO [2022-03-16 20:10:12] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
SUCCESS [2022-03-16 20:10:13] ==========================================================
SUCCESS [2022-03-16 20:10:13] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2022-03-16 20:10:13] ==========================================================
INFO [2022-03-16 20:10:13]    >> 2 read(s) created from FASTA file.
INFO [2022-03-16 20:10:13]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2022-03-16 20:10:13]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
DEBUG [2022-03-16 20:10:13]    >> For more information, please run 'object'
DEBUG [2022-03-16 20:10:13]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2022-03-16 20:10:13] ========================================================
INFO [2022-03-16 20:10:13] ================ Creating 'SangerContig' ===============
INFO [2022-03-16 20:10:13] ========================================================
INFO [2022-03-16 20:10:13]   >> Contig Name: 'Achl_RBNII384-13'
INFO [2022-03-16 20:10:13]   >> You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2022-03-16 20:10:13] >> Your contig name is Achl_RBNII384-13
SUCCESS [2022-03-16 20:10:13] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:13] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:13] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:13]    >> 'Achl_RBNII384-13_1_F' is created (Forward Read; FASTA).
SUCCESS [2022-03-16 20:10:13] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:13] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:13] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:13]    >> 'Achl_RBNII384-13_2_R' is created (Reverse Read; FASTA).
INFO [2022-03-16 20:10:13]    >> The number of reads detected: 2
INFO [2022-03-16 20:10:13] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
SUCCESS [2022-03-16 20:10:14] ==========================================================
SUCCESS [2022-03-16 20:10:14] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2022-03-16 20:10:14] ==========================================================
INFO [2022-03-16 20:10:14]    >> 2 read(s) created from FASTA file.
INFO [2022-03-16 20:10:14]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2022-03-16 20:10:14]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
DEBUG [2022-03-16 20:10:14]    >> For more information, please run 'object'
DEBUG [2022-03-16 20:10:14]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2022-03-16 20:10:14] ------------------------------------------------
INFO [2022-03-16 20:10:14] -------- Creating 'SangerRead' instance --------
INFO [2022-03-16 20:10:14] ------------------------------------------------
INFO [2022-03-16 20:10:14] >> Forward Read: Creating abif & sangerseq ...
INFO [2022-03-16 20:10:14]     >> Creating Forward Read raw abif ...
INFO [2022-03-16 20:10:14]     >> Creating Forward Read raw sangerseq ...
INFO [2022-03-16 20:10:14]           * Making basecall !!
INFO [2022-03-16 20:10:14]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2022-03-16 20:10:15] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:15] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:15] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:15]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2022-03-16 20:10:15]    >> Read is trimmed by 'M1 - Mott’s trimming algorithm'.
DEBUG [2022-03-16 20:10:15]    >> For more information, please run 'object'.
DEBUG [2022-03-16 20:10:15]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2022-03-16 20:10:15] ------------------------------------------------
INFO [2022-03-16 20:10:15] -------- Creating 'SangerRead' instance --------
INFO [2022-03-16 20:10:15] ------------------------------------------------
INFO [2022-03-16 20:10:15] >> Reverse Read: Creating abif & sangerseq ...
INFO [2022-03-16 20:10:15]     >> Creating Reverse Read raw abif ...
INFO [2022-03-16 20:10:15]     >> Creating Reverse Read raw sangerseq ...
INFO [2022-03-16 20:10:15]           * Making basecall !!
INFO [2022-03-16 20:10:15]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2022-03-16 20:10:15] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:15] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:15] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:15]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2022-03-16 20:10:15]    >> Read is trimmed by 'M1 - Mott’s trimming algorithm'.
DEBUG [2022-03-16 20:10:15]    >> For more information, please run 'object'.
DEBUG [2022-03-16 20:10:15]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2022-03-16 20:10:15] ------------------------------------------------
INFO [2022-03-16 20:10:15] -------- Creating 'SangerRead' instance --------
INFO [2022-03-16 20:10:15] ------------------------------------------------
INFO [2022-03-16 20:10:15] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2022-03-16 20:10:15] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:15] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:15] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:15]    >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
INFO [2022-03-16 20:10:15]    >> Read is trimmed by 'M1 - Mott’s trimming algorithm'.
DEBUG [2022-03-16 20:10:15]    >> For more information, please run 'object'.
DEBUG [2022-03-16 20:10:15]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2022-03-16 20:10:15] ------------------------------------------------
INFO [2022-03-16 20:10:15] -------- Creating 'SangerRead' instance --------
INFO [2022-03-16 20:10:15] ------------------------------------------------
INFO [2022-03-16 20:10:15] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2022-03-16 20:10:15] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:15] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2022-03-16 20:10:15] --------------------------------------------------------
SUCCESS [2022-03-16 20:10:15]    >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2022-03-16 20:10:15]    >> Read is trimmed by 'M1 - Mott’s trimming algorithm'.
DEBUG [2022-03-16 20:10:16]    >> For more information, please run 'object'.
DEBUG [2022-03-16 20:10:16]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
ERROR [2022-03-16 20:10:16] FILE_NOT_EXIST_ERROR
'D:/biocbuild/bbs-3.15-bioc/R/library/sangeranalyseR/extdata/Allolobophora_chlorotica/ACHLO/TEST_Achl_ACHLO006-09_2_R.ab1' file does not exist.
DEBUG [2022-03-16 20:10:16]    >> For more information, please run 'object'.
DEBUG [2022-03-16 20:10:16]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
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 0.05 secs
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
INFO [2022-03-16 20:10:22] Aligning consensus reads ... 
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
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
INFO [2022-03-16 20:10:30] Aligning consensus reads ... 
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
INFO [2022-03-16 20:10:34]           * Making basecall !!
INFO [2022-03-16 20:10:34]           * Updating slots in 'SangerRead' instance !!
INFO [2022-03-16 20:10:34]           * Making basecall !!
INFO [2022-03-16 20:10:34]           * Updating slots in 'SangerRead' instance !!
INFO [2022-03-16 20:10:34]           * Making basecall !!
INFO [2022-03-16 20:10:35]           * Updating slots in 'SangerRead' instance !!
INFO [2022-03-16 20:10:35]           * Making basecall !!
INFO [2022-03-16 20:10:35]           * Updating slots in 'SangerRead' instance !!
INFO [2022-03-16 20:10:35]           * Making basecall !!
INFO [2022-03-16 20:10:35]           * Updating slots in 'SangerRead' instance !!
INFO [2022-03-16 20:10:37] >>> outputDir : D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQ3aj58
INFO [2022-03-16 20:10:37] Start writing 'D:/biocbuild/bbs-3.15-bioc/R/library/sangeranalyseR/extdata/Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1' to FASTA format ...
INFO [2022-03-16 20:10:37] >> 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQ3aj58/Achl_ACHLO006-09_1_F.fa' is written
INFO [2022-03-16 20:10:37] >>> outputDir : D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQ3aj58
INFO [2022-03-16 20:10:37] Start writing 'D:/biocbuild/bbs-3.15-bioc/R/library/sangeranalyseR/extdata/fasta/SangerRead/Achl_ACHLO006-09_1_F.fa' to FASTA format ...
INFO [2022-03-16 20:10:37] >> 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQ3aj58/Achl_ACHLO006-09_1_F.fa' is written
INFO [2022-03-16 20:10:37] >>> outputDir : D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQ3aj58
INFO [2022-03-16 20:10:37] Start writing 'D:/biocbuild/bbs-3.15-bioc/R/library/sangeranalyseR/extdata/fasta/SangerRead/Achl_ACHLO006-09_2_R.fa' to FASTA format ...
INFO [2022-03-16 20:10:37] >> 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQ3aj58/Achl_ACHLO006-09_2_R.fa' is written
INFO [2022-03-16 20:10:37] Aligning consensus reads ... 
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
INFO [2022-03-16 20:10:39]           * Making basecall !!
INFO [2022-03-16 20:10:39]           * Updating slots in 'SangerRead' instance !!
INFO [2022-03-16 20:10:39]           * Making basecall !!
INFO [2022-03-16 20:10:40]           * Updating slots in 'SangerRead' instance !!
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 899 ]
> 
> proc.time()
   user  system elapsed 
  54.51    1.18   55.75 

Example timings

sangeranalyseR.Rcheck/sangeranalyseR-Ex.timings

nameusersystemelapsed
ChromatogramParam-class000
MakeBaseCalls-methods0.470.030.50
ObjectResults-class000
QualityReport-class-qualityBasePlot000
QualityReport-class-updateQualityParam0.000.010.01
QualityReport-class0.400.020.42
SangerAlignment-class-generateReportSA0.040.020.05
SangerAlignment-class-launchAppSA0.040.010.06
SangerAlignment-class-updateQualityParam0.410.020.42
SangerAlignment-class-writeFastaSA0.060.010.08
SangerAlignment-class41.94 0.6942.66
SangerAlignment7.890.118.09
SangerContig-class-generateReportSC0.010.000.02
SangerContig-class-launchAppSC0.040.010.04
SangerContig-class-readTable0.110.020.13
SangerContig-class-updateQualityParam0.010.020.03
SangerContig-class-writeFastaSC0.080.000.08
SangerContig-class9.220.079.30
SangerContig0.080.000.07
SangerRead-class-MakeBaseCalls0.390.000.39
SangerRead-class-generateReportSR0.030.000.04
SangerRead-class-qualityBasePlot0.010.000.01
SangerRead-class-readTable0.080.040.11
SangerRead-class-updateQualityParam0.220.000.22
SangerRead-class-writeFastaSR0.030.000.03
SangerRead-class1.640.001.64
SangerRead0.410.000.41
generateReport0.080.030.11
generateReportSA-methods0.030.010.04
generateReportSC-methods0.010.020.04
generateReportSR-methods0.020.010.03
launchApp0.060.020.07
launchAppSA-methods0.060.000.08
launchAppSC-methods0.040.010.05
qualityBasePlot-methods0.250.110.36
readTable-methods0.070.040.11
updateQualityParam-methods0.070.060.12
writeFasta0.120.000.13
writeFastaSA-methods0.090.010.11
writeFastaSC-methods0.080.000.08
writeFastaSR-methods0.050.020.06