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CHECK report for sangeranalyseR on tokay1

This page was generated on 2021-05-06 12:33:25 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the sangeranalyseR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1616/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sangeranalyseR 1.0.0  (landing page)
Kuan-Hao Chao
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/sangeranalyseR
Branch: RELEASE_3_12
Last Commit: d1a14ae
Last Changed Date: 2020-10-27 11:57:35 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: sangeranalyseR
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sangeranalyseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings sangeranalyseR_1.0.0.tar.gz
StartedAt: 2021-05-06 06:34:39 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:45:25 -0400 (Thu, 06 May 2021)
EllapsedTime: 645.4 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: sangeranalyseR.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sangeranalyseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings sangeranalyseR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/sangeranalyseR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.0.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'stringr', 'ape', 'Biostrings', 'DECIPHER', 'parallel', 'reshape2',
  'phangorn', 'sangerseqR', 'gridExtra', 'shiny', 'shinydashboard',
  'shinyjs', 'data.table', 'plotly', 'DT', 'zeallot', 'excelR',
  'shinycssloaders', 'ggdendro', 'shinyWidgets', 'openxlsx', 'tools',
  'rmarkdown', 'kableExtra', 'seqinr', 'BiocStyle', 'logger'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
  docs/build/html/.buildinfo
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... WARNING
Found the following file with a non-portable file name:
  docs/wallpaperflare.com_wallpaper (1).jpg
These are not fully portable file names.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'sangeranalyseR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    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 ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'BiocStyle' 'phangorn' 'reshape2' 'zeallot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SangerAlignment: no visible global function definition for 'new'
SangerAlignmentServer: no visible binding for '<<-' assignment to
  'NEW_SANGER_ALIGNED_CONSENSUS_READ_SET'
SangerAlignmentServer: no visible global function definition for
  'colorRamp'
SangerContig: no visible global function definition for 'new'
SangerContigServer: no visible binding for '<<-' assignment to
  'NEW_SANGER_CONTIG'
SangerContigServer: no visible global function definition for
  'colorRamp'
SangerRead: no visible global function definition for 'new'
alignContigs: no visible global function definition for 'as.phylo'
alignContigs: no visible global function definition for 'rtree'
checkAb1FastaCsv: no visible global function definition for 'read.csv'
chromatogram_overwrite: no visible global function definition for 'rgb'
chromatogram_overwrite: no visible global function definition for 'par'
chromatogram_overwrite: no visible global function definition for
  'quantile'
chromatogram_overwrite: no visible global function definition for 'IQR'
chromatogram_overwrite: no visible global function definition for 'pdf'
chromatogram_overwrite: no visible global function definition for
  'rect'
chromatogram_overwrite: no visible global function definition for
  'lines'
chromatogram_overwrite: no visible global function definition for
  'mtext'
chromatogram_overwrite: no visible global function definition for
  'axis'
chromatogram_overwrite: no visible global function definition for
  'dev.off'
primarySeqDisplay: no visible global function definition for 'rgb'
primarySeqTrimmedDisplay: no visible global function definition for
  'rgb'
secondSeqTrimmedDisplay: no visible global function definition for
  'rgb'
secondarySeqDisplay: no visible global function definition for 'rgb'
initialize,ChromatogramParam: no visible global function definition for
  'callNextMethod'
initialize,QualityReport: no visible global function definition for
  'callNextMethod'
initialize,SangerAlignment: no visible global function definition for
  'str_split'
initialize,SangerAlignment : <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
  'callNextMethod'
initialize,SangerContig: no visible global function definition for
  'read.csv'
initialize,SangerContig : <anonymous>: no visible global function
  definition for 'new'
initialize,SangerContig: no visible global function definition for
  'callNextMethod'
initialize,SangerRead: no visible global function definition for 'new'
initialize,SangerRead: no visible global function definition for
  'isEmpty'
initialize,SangerRead: no visible global function definition for
  'callNextMethod'
launchAppSA,SangerAlignment: no visible global function definition for
  'shinyOptions'
launchAppSA,SangerAlignment: no visible global function definition for
  'shinyApp'
launchAppSC,SangerContig: no visible global function definition for
  'shinyOptions'
launchAppSC,SangerContig: no visible global function definition for
  'shinyApp'
Undefined global functions or variables:
  IQR as.phylo axis callNextMethod colorRamp dev.off isEmpty lines
  mtext new par pdf quantile read.csv rect rgb rtree shinyApp
  shinyOptions str_split
Consider adding
  importFrom("grDevices", "colorRamp", "dev.off", "pdf", "rgb")
  importFrom("graphics", "axis", "lines", "mtext", "par", "rect")
  importFrom("methods", "callNextMethod", "new")
  importFrom("stats", "IQR", "quantile")
  importFrom("utils", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'readTable' and siglist 'SangerContig'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'SangerAlignment-class-generateReportSA':
\S4method{generateReportSA}{SangerAlignment}
  Code: function(object, outputDir, includeSangerContig = TRUE,
                 includeSangerRead = TRUE, colors)
  Docs: function(object, outputDir, includeSangerContig = TRUE,
                 includeSangerRead = TRUE)
  Argument names in code not in docs:
    colors

Codoc mismatches from documentation object 'SangerAlignment-class-launchAppSA':
\S4method{launchAppSA}{SangerAlignment}
  Code: function(object, outputDir = NULL, colors = "default")
  Docs: function(object, outputDir = NULL)
  Argument names in code not in docs:
    colors

Codoc mismatches from documentation object 'SangerContig-class-generateReportSC':
\S4method{generateReportSC}{SangerContig}
  Code: function(object, outputDir, includeSangerRead = TRUE, colors,
                 navigationAlignmentFN = NULL)
  Docs: function(object, outputDir, includeSangerRead = TRUE,
                 navigationAlignmentFN = NULL)
  Argument names in code not in docs:
    colors
  Mismatches in argument names:
    Position: 4 Code: colors Docs: navigationAlignmentFN

Codoc mismatches from documentation object 'SangerContig-class-launchAppSC':
\S4method{launchAppSC}{SangerContig}
  Code: function(object, outputDir = NULL, colors = "default")
  Docs: function(object, outputDir = NULL)
  Argument names in code not in docs:
    colors

Codoc mismatches from documentation object 'SangerRead-class-generateReportSR':
\S4method{generateReportSR}{SangerRead}
  Code: function(object, outputDir, colors, navigationContigFN = NULL,
                 navigationAlignmentFN = NULL)
  Docs: function(object, outputDir, navigationContigFN = NULL,
                 navigationAlignmentFN = NULL)
  Argument names in code not in docs:
    colors
  Mismatches in argument names:
    Position: 3 Code: colors Docs: navigationContigFN
    Position: 4 Code: navigationContigFN Docs: navigationAlignmentFN

Codoc mismatches from documentation object 'generateReport':
generateReport
  Code: function(object, outputDir = NULL, includeSangerContig = TRUE,
                 includeSangerRead = TRUE, colors = "default", ...)
  Docs: function(object, outputDir = NULL, includeSangerContig = TRUE,
                 includeSangerRead = TRUE, ...)
  Argument names in code not in docs:
    colors
  Mismatches in argument names:
    Position: 5 Code: colors Docs: ...

Codoc mismatches from documentation object 'generateReportSA':
generateReportSA
  Code: function(object, outputDir = NULL, includeSangerContig = TRUE,
                 includeSangerRead = TRUE, colors = "default", ...)
  Docs: function(object, outputDir = NULL, includeSangerContig = TRUE,
                 includeSangerRead = TRUE, ...)
  Argument names in code not in docs:
    colors
  Mismatches in argument names:
    Position: 5 Code: colors Docs: ...

Codoc mismatches from documentation object 'generateReportSC':
generateReportSC
  Code: function(object, outputDir = NULL, includeSangerRead = TRUE,
                 colors = "default", ...)
  Docs: function(object, outputDir = NULL, includeSangerRead = TRUE,
                 ...)
  Argument names in code not in docs:
    colors
  Mismatches in argument names:
    Position: 4 Code: colors Docs: ...

Codoc mismatches from documentation object 'generateReportSR':
generateReportSR
  Code: function(object, outputDir = NULL, colors = "default", ...)
  Docs: function(object, outputDir = NULL, ...)
  Argument names in code not in docs:
    colors
  Mismatches in argument names:
    Position: 3 Code: colors Docs: ...

Codoc mismatches from documentation object 'launchApp':
launchApp
  Code: function(object, outputDir = NULL, colors = "default")
  Docs: function(object, outputDir = NULL)
  Argument names in code not in docs:
    colors

Codoc mismatches from documentation object 'launchAppSA':
launchAppSA
  Code: function(object, outputDir = NULL, colors = "default")
  Docs: function(object, outputDir = NULL)
  Argument names in code not in docs:
    colors

Codoc mismatches from documentation object 'launchAppSC':
launchAppSC
  Code: function(object, outputDir = NULL, colors = "default")
  Docs: function(object, outputDir = NULL)
  Argument names in code not in docs:
    colors

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
SangerAlignment-class 58.89   0.69   59.72
SangerAlignment       16.83   0.25   17.79
SangerContig-class    12.56   0.08   12.65
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
SangerAlignment-class 46.65   0.47   47.16
SangerAlignment       12.78   0.18   13.00
SangerContig-class    12.14   0.05   12.19
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 3 WARNINGs, 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/sangeranalyseR.Rcheck/00check.log'
for details.

Installation output

sangeranalyseR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/sangeranalyseR_1.0.0.tar.gz && rm -rf sangeranalyseR.buildbin-libdir && mkdir sangeranalyseR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sangeranalyseR.buildbin-libdir sangeranalyseR_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL sangeranalyseR_1.0.0.zip && rm sangeranalyseR_1.0.0.tar.gz sangeranalyseR_1.0.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1 35.5M    1  470k    0     0  2306k      0  0:00:15 --:--:--  0:00:15 2316k
100 35.5M  100 35.5M    0     0  55.4M      0 --:--:-- --:--:-- --:--:-- 55.5M

install for i386

* 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  
    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-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

install for x64

* installing *source* package 'sangeranalyseR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sangeranalyseR' as sangeranalyseR_1.0.0.zip
* DONE (sangeranalyseR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'sangeranalyseR' successfully unpacked and MD5 sums checked

Tests output

sangeranalyseR.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: XVector

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: 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: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: kableExtra
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 [2021-05-06 06:42:15] *************************************************
INFO [2021-05-06 06:42:15] **** Start creating SangerAlignment instance ****
INFO [2021-05-06 06:42:15] *************************************************
INFO [2021-05-06 06:42:15] **** You are using Regex Method to group AB1 files!
INFO [2021-05-06 06:42:15] ******** Contig Name: Achl_ACHLO006-09
INFO [2021-05-06 06:42:15] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 06:42:15] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:42:15]     * Creating Forward Read raw abif ...
INFO [2021-05-06 06:42:15]     * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 06:42:15]           * Making basecall !!
INFO [2021-05-06 06:42:15]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:42:16]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:16] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:42:16]     * Creating Reverse Read raw abif ...
INFO [2021-05-06 06:42:16]     * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 06:42:16]           * Making basecall !!
INFO [2021-05-06 06:42:17]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:42:17]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:17] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.06 secs
SUCCESS [2021-05-06 06:42:19]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:42:19] ******** Contig Name: Achl_ACHLO007-09
INFO [2021-05-06 06:42:19] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 06:42:19] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:42:19]     * Creating Forward Read raw abif ...
INFO [2021-05-06 06:42:19]     * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 06:42:19]           * Making basecall !!
INFO [2021-05-06 06:42:20]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:42:20]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:20] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:42:20]     * Creating Reverse Read raw abif ...
INFO [2021-05-06 06:42:20]     * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 06:42:20]           * Making basecall !!
INFO [2021-05-06 06:42:20]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:42:21]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:21] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
SUCCESS [2021-05-06 06:42:22]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:42:22] ******** Contig Name: Achl_ACHLO040-09
INFO [2021-05-06 06:42:22] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 06:42:22] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:42:22]     * Creating Forward Read raw abif ...
INFO [2021-05-06 06:42:23]     * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 06:42:23]           * Making basecall !!
INFO [2021-05-06 06:42:23]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:42:23]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:23] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:42:23]     * Creating Reverse Read raw abif ...
INFO [2021-05-06 06:42:23]     * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 06:42:23]           * Making basecall !!
INFO [2021-05-06 06:42:23]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:42:24]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:24] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
SUCCESS [2021-05-06 06:42:26]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:42:26] ******** Contig Name: Achl_ACHLO041-09
INFO [2021-05-06 06:42:26] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 06:42:26] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:42:26]     * Creating Forward Read raw abif ...
INFO [2021-05-06 06:42:26]     * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 06:42:26]           * Making basecall !!
INFO [2021-05-06 06:42:26]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:42:26]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:26] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:42:26]     * Creating Reverse Read raw abif ...
INFO [2021-05-06 06:42:26]     * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 06:42:26]           * Making basecall !!
INFO [2021-05-06 06:42:26]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:42:27]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:27] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
SUCCESS [2021-05-06 06:42:28]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:42:28] Aligning consensus reads ... 
SUCCESS [2021-05-06 06:42:29]   >> 'SangerAlignment' S4 instance is created !!
INFO [2021-05-06 06:42:30] *************************************************
INFO [2021-05-06 06:42:30] **** Start creating SangerAlignment instance ****
INFO [2021-05-06 06:42:30] *************************************************
INFO [2021-05-06 06:42:30] **** You are using CSV Name Conversion Method to group reads in FASTA file (with CSV file)!
INFO [2021-05-06 06:42:30] ******** Contig Name: Achl_ACHLO006-09
INFO [2021-05-06 06:42:30] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 06:42:30] **** Your contig name is Achl_ACHLO006-09
INFO [2021-05-06 06:42:30] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:42:30]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:30] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:42:30]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:30] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
SUCCESS [2021-05-06 06:42:32]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:42:32] ******** Contig Name: Achl_ACHLO007-09
INFO [2021-05-06 06:42:32] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 06:42:32] **** Your contig name is Achl_ACHLO007-09
INFO [2021-05-06 06:42:32] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:42:33]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:33] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:42:33]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:33] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
SUCCESS [2021-05-06 06:42:34]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:42:34] ******** Contig Name: Achl_ACHLO040-09
INFO [2021-05-06 06:42:34] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 06:42:35] **** Your contig name is Achl_ACHLO040-09
INFO [2021-05-06 06:42:35] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:42:35]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:35] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:42:35]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:35] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
SUCCESS [2021-05-06 06:42:37]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:42:37] ******** Contig Name: Achl_ACHLO041-09
INFO [2021-05-06 06:42:37] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 06:42:37] **** Your contig name is Achl_ACHLO041-09
INFO [2021-05-06 06:42:37] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:42:37]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:37] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:42:37]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:37] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
SUCCESS [2021-05-06 06:42:39]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:42:39] Aligning consensus reads ... 
SUCCESS [2021-05-06 06:42:40]   >> 'SangerAlignment' S4 instance is created !!
INFO [2021-05-06 06:42:40] ******** Contig Name: Achl_ACHLO006-09
INFO [2021-05-06 06:42:40] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 06:42:40] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:42:40]     * Creating Forward Read raw abif ...
INFO [2021-05-06 06:42:40]     * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 06:42:40]           * Making basecall !!
INFO [2021-05-06 06:42:40]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:42:41]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:41] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:42:41]     * Creating Reverse Read raw abif ...
INFO [2021-05-06 06:42:41]     * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 06:42:41]           * Making basecall !!
INFO [2021-05-06 06:42:41]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:42:41]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:41] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.06 secs
SUCCESS [2021-05-06 06:42:44]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:42:44] ******** Contig Name: Achl_RBNII384-13
INFO [2021-05-06 06:42:44] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 06:42:44] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:42:44]     * Creating Forward Read raw abif ...
INFO [2021-05-06 06:42:44]     * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 06:42:44]           * Making basecall !!
INFO [2021-05-06 06:42:44]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:42:44]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:44] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:42:44]     * Creating Reverse Read raw abif ...
INFO [2021-05-06 06:42:45]     * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 06:42:45]           * Making basecall !!
INFO [2021-05-06 06:42:45]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:42:45]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:45] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
SUCCESS [2021-05-06 06:42:47]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:42:47] ******** Contig Name: Achl_ACHLO006-09
INFO [2021-05-06 06:42:47] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 06:42:47] **** Your contig name is Achl_ACHLO006-09
INFO [2021-05-06 06:42:47] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:42:48]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:48] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:42:48]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:48] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
SUCCESS [2021-05-06 06:42:50]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:42:50] ******** Contig Name: Achl_RBNII384-13
INFO [2021-05-06 06:42:50] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 06:42:50] **** Your contig name is Achl_RBNII384-13
INFO [2021-05-06 06:42:50] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:42:51]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:51] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:42:51]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:51] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.06 secs
SUCCESS [2021-05-06 06:42:54]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:42:54] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:42:54]     * Creating Forward Read raw abif ...
INFO [2021-05-06 06:42:54]     * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 06:42:54]           * Making basecall !!
INFO [2021-05-06 06:42:54]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:42:54]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:54] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:42:55]     * Creating Reverse Read raw abif ...
INFO [2021-05-06 06:42:55]     * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 06:42:55]           * Making basecall !!
INFO [2021-05-06 06:42:55]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:42:55]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:55] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:42:56]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:56] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:42:56]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:42:57] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
INFO [2021-05-06 06:42:59] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
INFO [2021-05-06 06:43:02] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
INFO [2021-05-06 06:43:04] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
INFO [2021-05-06 06:43:06] Aligning consensus reads ... 
INFO [2021-05-06 06:43:07] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
INFO [2021-05-06 06:43:10] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
INFO [2021-05-06 06:43:12] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
INFO [2021-05-06 06:43:14] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
INFO [2021-05-06 06:43:15] Aligning consensus reads ... 
INFO [2021-05-06 06:43:17] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
INFO [2021-05-06 06:43:19] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
INFO [2021-05-06 06:43:21]           * Making basecall !!
INFO [2021-05-06 06:43:21]           * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 06:43:21]           * Making basecall !!
INFO [2021-05-06 06:43:22]           * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 06:43:22]           * Making basecall !!
INFO [2021-05-06 06:43:22]           * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 06:43:22]           * Making basecall !!
INFO [2021-05-06 06:43:23]           * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 06:43:23]           * Making basecall !!
INFO [2021-05-06 06:43:23]           * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 06:43:26] >>> outputDir : C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpoJhsNG
INFO [2021-05-06 06:43:26] Start writing 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/sangeranalyseR/extdata/Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1' to FASTA format ...
INFO [2021-05-06 06:43:26] >> 'C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpoJhsNG/Achl_ACHLO006-09_1_F.fa' is written
INFO [2021-05-06 06:43:26] >>> outputDir : C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpoJhsNG
INFO [2021-05-06 06:43:26] Start writing 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/sangeranalyseR/extdata/fasta/SangerRead/Achl_ACHLO006-09_1_F.fa' to FASTA format ...
INFO [2021-05-06 06:43:26] >> 'C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpoJhsNG/Achl_ACHLO006-09_1_F.fa' is written
INFO [2021-05-06 06:43:26] >>> outputDir : C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpoJhsNG
INFO [2021-05-06 06:43:26] Start writing 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/sangeranalyseR/extdata/fasta/SangerRead/Achl_ACHLO006-09_2_R.fa' to FASTA format ...
INFO [2021-05-06 06:43:26] >> 'C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpoJhsNG/Achl_ACHLO006-09_2_R.fa' is written
INFO [2021-05-06 06:43:27] Aligning consensus reads ... 
INFO [2021-05-06 06:43:27] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
INFO [2021-05-06 06:43:29]           * Making basecall !!
INFO [2021-05-06 06:43:29]           * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 06:43:29]           * Making basecall !!
INFO [2021-05-06 06:43:29]           * Updating slots in 'SangerRead' instance !!
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 930 ]
> 
> proc.time()
   user  system elapsed 
  83.09    1.54   84.73

sangeranalyseR.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: XVector

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: 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: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

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    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: kableExtra
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 [2021-05-06 06:43:39] *************************************************
INFO [2021-05-06 06:43:39] **** Start creating SangerAlignment instance ****
INFO [2021-05-06 06:43:39] *************************************************
INFO [2021-05-06 06:43:39] **** You are using Regex Method to group AB1 files!
INFO [2021-05-06 06:43:39] ******** Contig Name: Achl_ACHLO006-09
INFO [2021-05-06 06:43:39] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 06:43:39] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:43:39]     * Creating Forward Read raw abif ...
INFO [2021-05-06 06:43:39]     * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 06:43:39]           * Making basecall !!
INFO [2021-05-06 06:43:39]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:43:40]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:43:40] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:43:40]     * Creating Reverse Read raw abif ...
INFO [2021-05-06 06:43:40]     * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 06:43:40]           * Making basecall !!
INFO [2021-05-06 06:43:40]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:43:40]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:43:40] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.06 secs
SUCCESS [2021-05-06 06:43:42]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:43:43] ******** Contig Name: Achl_ACHLO007-09
INFO [2021-05-06 06:43:43] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 06:43:43] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:43:43]     * Creating Forward Read raw abif ...
INFO [2021-05-06 06:43:43]     * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 06:43:43]           * Making basecall !!
INFO [2021-05-06 06:43:43]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:43:43]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:43:43] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:43:43]     * Creating Reverse Read raw abif ...
INFO [2021-05-06 06:43:43]     * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 06:43:43]           * Making basecall !!
INFO [2021-05-06 06:43:44]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:43:44]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:43:44] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.06 secs
SUCCESS [2021-05-06 06:43:46]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:43:46] ******** Contig Name: Achl_ACHLO040-09
INFO [2021-05-06 06:43:46] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 06:43:46] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:43:46]     * Creating Forward Read raw abif ...
INFO [2021-05-06 06:43:47]     * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 06:43:47]           * Making basecall !!
INFO [2021-05-06 06:43:47]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:43:48]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:43:48] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:43:48]     * Creating Reverse Read raw abif ...
INFO [2021-05-06 06:43:48]     * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 06:43:48]           * Making basecall !!
INFO [2021-05-06 06:43:48]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:43:49]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:43:49] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.06 secs
SUCCESS [2021-05-06 06:43:51]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:43:51] ******** Contig Name: Achl_ACHLO041-09
INFO [2021-05-06 06:43:51] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 06:43:51] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:43:51]     * Creating Forward Read raw abif ...
INFO [2021-05-06 06:43:51]     * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 06:43:51]           * Making basecall !!
INFO [2021-05-06 06:43:52]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:43:52]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:43:52] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:43:52]     * Creating Reverse Read raw abif ...
INFO [2021-05-06 06:43:52]     * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 06:43:52]           * Making basecall !!
INFO [2021-05-06 06:43:52]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:43:53]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:43:53] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
SUCCESS [2021-05-06 06:43:55]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:43:55] Aligning consensus reads ... 
SUCCESS [2021-05-06 06:43:56]   >> 'SangerAlignment' S4 instance is created !!
INFO [2021-05-06 06:43:56] *************************************************
INFO [2021-05-06 06:43:56] **** Start creating SangerAlignment instance ****
INFO [2021-05-06 06:43:56] *************************************************
INFO [2021-05-06 06:43:56] **** You are using CSV Name Conversion Method to group reads in FASTA file (with CSV file)!
INFO [2021-05-06 06:43:56] ******** Contig Name: Achl_ACHLO006-09
INFO [2021-05-06 06:43:56] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 06:43:56] **** Your contig name is Achl_ACHLO006-09
INFO [2021-05-06 06:43:56] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:43:57]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:43:57] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:43:57]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:43:57] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
SUCCESS [2021-05-06 06:43:59]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:43:59] ******** Contig Name: Achl_ACHLO007-09
INFO [2021-05-06 06:43:59] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 06:43:59] **** Your contig name is Achl_ACHLO007-09
INFO [2021-05-06 06:43:59] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:44:00]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:00] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:44:00]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:00] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.06 secs
SUCCESS [2021-05-06 06:44:02]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:44:02] ******** Contig Name: Achl_ACHLO040-09
INFO [2021-05-06 06:44:02] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 06:44:02] **** Your contig name is Achl_ACHLO040-09
INFO [2021-05-06 06:44:02] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:44:02]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:02] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:44:03]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:03] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
SUCCESS [2021-05-06 06:44:05]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:44:05] ******** Contig Name: Achl_ACHLO041-09
INFO [2021-05-06 06:44:05] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 06:44:05] **** Your contig name is Achl_ACHLO041-09
INFO [2021-05-06 06:44:05] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:44:05]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:05] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:44:06]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:06] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.03 secs
SUCCESS [2021-05-06 06:44:07]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:44:07] Aligning consensus reads ... 
SUCCESS [2021-05-06 06:44:08]   >> 'SangerAlignment' S4 instance is created !!
INFO [2021-05-06 06:44:08] ******** Contig Name: Achl_ACHLO006-09
INFO [2021-05-06 06:44:08] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 06:44:08] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:44:08]     * Creating Forward Read raw abif ...
INFO [2021-05-06 06:44:08]     * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 06:44:08]           * Making basecall !!
INFO [2021-05-06 06:44:08]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:44:09]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:09] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:44:09]     * Creating Reverse Read raw abif ...
INFO [2021-05-06 06:44:09]     * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 06:44:09]           * Making basecall !!
INFO [2021-05-06 06:44:09]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:44:10]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:10] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.06 secs
SUCCESS [2021-05-06 06:44:12]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:44:12] ******** Contig Name: Achl_RBNII384-13
INFO [2021-05-06 06:44:12] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 06:44:12] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:44:12]     * Creating Forward Read raw abif ...
INFO [2021-05-06 06:44:12]     * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 06:44:12]           * Making basecall !!
INFO [2021-05-06 06:44:12]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:44:13]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:13] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:44:13]     * Creating Reverse Read raw abif ...
INFO [2021-05-06 06:44:13]     * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 06:44:13]           * Making basecall !!
INFO [2021-05-06 06:44:13]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:44:13]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:13] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.06 secs
SUCCESS [2021-05-06 06:44:16]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:44:16] ******** Contig Name: Achl_ACHLO006-09
INFO [2021-05-06 06:44:16] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 06:44:16] **** Your contig name is Achl_ACHLO006-09
INFO [2021-05-06 06:44:16] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:44:16]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:16] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:44:16]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:16] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
SUCCESS [2021-05-06 06:44:19]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:44:19] ******** Contig Name: Achl_RBNII384-13
INFO [2021-05-06 06:44:19] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 06:44:19] **** Your contig name is Achl_RBNII384-13
INFO [2021-05-06 06:44:19] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:44:19]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:19] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:44:20]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:20] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
SUCCESS [2021-05-06 06:44:22]   >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 06:44:22] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:44:22]     * Creating Forward Read raw abif ...
INFO [2021-05-06 06:44:22]     * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 06:44:22]           * Making basecall !!
INFO [2021-05-06 06:44:23]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:44:23]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:23] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 06:44:23]     * Creating Reverse Read raw abif ...
INFO [2021-05-06 06:44:23]     * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 06:44:23]           * Making basecall !!
INFO [2021-05-06 06:44:24]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 06:44:24]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:24] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:44:24]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:24] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 06:44:25]   >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 06:44:27] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
INFO [2021-05-06 06:44:31] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.06 secs
INFO [2021-05-06 06:44:35] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.06 secs
INFO [2021-05-06 06:44:38] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.08 secs
INFO [2021-05-06 06:44:41] Aligning consensus reads ... 
INFO [2021-05-06 06:44:44] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.06 secs
INFO [2021-05-06 06:44:47] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.06 secs
INFO [2021-05-06 06:44:50] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.05 secs
INFO [2021-05-06 06:44:53] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.06 secs
INFO [2021-05-06 06:44:56] Aligning consensus reads ... 
INFO [2021-05-06 06:44:59] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.06 secs
INFO [2021-05-06 06:45:02] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.08 secs
INFO [2021-05-06 06:45:05]           * Making basecall !!
INFO [2021-05-06 06:45:05]           * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 06:45:06]           * Making basecall !!
INFO [2021-05-06 06:45:06]           * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 06:45:07]           * Making basecall !!
INFO [2021-05-06 06:45:07]           * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 06:45:07]           * Making basecall !!
INFO [2021-05-06 06:45:08]           * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 06:45:08]           * Making basecall !!
INFO [2021-05-06 06:45:08]           * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 06:45:12] >>> outputDir : C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmp2xu1t4
INFO [2021-05-06 06:45:12] Start writing 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/sangeranalyseR/extdata/Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1' to FASTA format ...
INFO [2021-05-06 06:45:12] >> 'C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmp2xu1t4/Achl_ACHLO006-09_1_F.fa' is written
INFO [2021-05-06 06:45:13] >>> outputDir : C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmp2xu1t4
INFO [2021-05-06 06:45:13] Start writing 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/sangeranalyseR/extdata/fasta/SangerRead/Achl_ACHLO006-09_1_F.fa' to FASTA format ...
INFO [2021-05-06 06:45:13] >> 'C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmp2xu1t4/Achl_ACHLO006-09_1_F.fa' is written
INFO [2021-05-06 06:45:13] >>> outputDir : C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmp2xu1t4
INFO [2021-05-06 06:45:13] Start writing 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/sangeranalyseR/extdata/fasta/SangerRead/Achl_ACHLO006-09_2_R.fa' to FASTA format ...
INFO [2021-05-06 06:45:13] >> 'C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmp2xu1t4/Achl_ACHLO006-09_2_R.fa' is written
INFO [2021-05-06 06:45:13] Aligning consensus reads ... 
INFO [2021-05-06 06:45:14] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================

Time difference of 0.06 secs
INFO [2021-05-06 06:45:17]           * Making basecall !!
INFO [2021-05-06 06:45:17]           * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 06:45:17]           * Making basecall !!
INFO [2021-05-06 06:45:17]           * Updating slots in 'SangerRead' instance !!
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 930 ]
> 
> proc.time()
   user  system elapsed 
 105.35    1.00  107.87

Example timings

sangeranalyseR.Rcheck/examples_i386/sangeranalyseR-Ex.timings

nameusersystemelapsed
ChromatogramParam-class000
MakeBaseCalls-methods0.840.030.88
QualityReport-class-qualityBasePlot0.000.020.01
QualityReport-class-updateQualityParam0.000.010.02
QualityReport-class0.690.020.73
SangerAlignment-class-generateReportSA0.090.010.11
SangerAlignment-class-launchAppSA0.110.040.14
SangerAlignment-class-updateQualityParam0.080.010.10
SangerAlignment-class-writeFastaSA0.110.000.11
SangerAlignment-class58.89 0.6959.72
SangerAlignment16.83 0.2517.79
SangerContig-class-generateReportSC0.030.010.05
SangerContig-class-launchAppSC0.050.000.05
SangerContig-class-updateQualityParam0.080.000.08
SangerContig-class-writeFastaSC0.120.000.12
SangerContig-class12.56 0.0812.65
SangerContig4.330.034.35
SangerRead-class-MakeBaseCalls0.770.030.80
SangerRead-class-generateReportSR0.030.020.05
SangerRead-class-qualityBasePlot0.050.000.05
SangerRead-class-readTable0.170.070.25
SangerRead-class-updateQualityParam0.480.020.50
SangerRead-class-writeFastaSR0.030.030.06
SangerRead-class2.490.012.50
SangerRead0.750.020.77
generateReport0.180.060.25
generateReportSA-methods0.100.020.11
generateReportSC-methods0.060.010.08
generateReportSR-methods0.030.030.06
launchApp0.140.050.19
launchAppSA-methods0.100.020.11
launchAppSC-methods0.060.010.07
qualityBasePlot-methods0.440.100.54
readTable-methods0.170.040.21
updateQualityParam-methods0.220.030.25
writeFasta0.150.030.19
writeFastaSA-methods0.130.000.13
writeFastaSC-methods0.060.000.06
writeFastaSR-methods0.060.000.06

sangeranalyseR.Rcheck/examples_x64/sangeranalyseR-Ex.timings

nameusersystemelapsed
ChromatogramParam-class000
MakeBaseCalls-methods0.710.010.73
QualityReport-class-qualityBasePlot0.000.020.02
QualityReport-class-updateQualityParam0.010.010.03
QualityReport-class0.860.030.89
SangerAlignment-class-generateReportSA0.050.020.06
SangerAlignment-class-launchAppSA0.080.000.08
SangerAlignment-class-updateQualityParam0.050.020.06
SangerAlignment-class-writeFastaSA0.100.030.14
SangerAlignment-class46.65 0.4747.16
SangerAlignment12.78 0.1813.00
SangerContig-class-generateReportSC0.030.020.05
SangerContig-class-launchAppSC0.040.000.04
SangerContig-class-updateQualityParam0.020.030.05
SangerContig-class-writeFastaSC0.060.000.06
SangerContig-class12.14 0.0512.19
SangerContig4.550.034.59
SangerRead-class-MakeBaseCalls0.480.000.49
SangerRead-class-generateReportSR0.040.000.03
SangerRead-class-qualityBasePlot0.010.010.03
SangerRead-class-readTable0.130.050.17
SangerRead-class-updateQualityParam0.390.000.39
SangerRead-class-writeFastaSR0.060.020.08
SangerRead-class2.780.012.80
SangerRead0.530.000.53
generateReport0.100.030.13
generateReportSA-methods0.060.000.06
generateReportSC-methods0.060.000.06
generateReportSR-methods0.050.000.05
launchApp0.120.030.15
launchAppSA-methods0.080.020.10
launchAppSC-methods0.060.020.08
qualityBasePlot-methods0.680.070.75
readTable-methods0.170.050.21
updateQualityParam-methods0.140.080.22
writeFasta0.120.010.14
writeFastaSA-methods0.100.020.11
writeFastaSC-methods0.060.000.07
writeFastaSR-methods0.030.000.04