CHECK report for sangeranalyseR on merida1
This page was generated on 2021-05-06 12:36:38 -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.
|
| 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) |
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |  | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | |
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | |
Summary
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sangeranalyseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sangeranalyseR_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/sangeranalyseR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sangeranalyseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sangeranalyseR’ version ‘1.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘sangeranalyseR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.1Mb
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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SangerAlignment-class 50.408 0.753 51.231
SangerAlignment 14.464 0.211 14.714
SangerContig-class 11.825 0.157 11.997
* 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: 3 WARNINGs, 6 NOTEs
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/sangeranalyseR.Rcheck/00check.log’
for details.
Installation output
sangeranalyseR.Rcheck/00install.out
Tests output
sangeranalyseR.Rcheck/tests/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-apple-darwin17.0 (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
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 05:54:13] *************************************************
INFO [2021-05-06 05:54:13] **** Start creating SangerAlignment instance ****
INFO [2021-05-06 05:54:13] *************************************************
INFO [2021-05-06 05:54:13] **** You are using Regex Method to group AB1 files!
INFO [2021-05-06 05:54:13] ******** Contig Name: Achl_ACHLO006-09
INFO [2021-05-06 05:54:13] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 05:54:13] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 05:54:13] * Creating Forward Read raw abif ...
INFO [2021-05-06 05:54:13] * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 05:54:13] * Making basecall !!
INFO [2021-05-06 05:54:13] * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 05:54:14] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:14] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 05:54:14] * Creating Reverse Read raw abif ...
INFO [2021-05-06 05:54:14] * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 05:54:14] * Making basecall !!
INFO [2021-05-06 05:54:14] * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 05:54:14] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:14] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.09 secs
SUCCESS [2021-05-06 05:54:17] >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 05:54:18] ******** Contig Name: Achl_ACHLO007-09
INFO [2021-05-06 05:54:18] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 05:54:18] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 05:54:18] * Creating Forward Read raw abif ...
INFO [2021-05-06 05:54:18] * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 05:54:18] * Making basecall !!
INFO [2021-05-06 05:54:18] * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 05:54:18] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:18] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 05:54:18] * Creating Reverse Read raw abif ...
INFO [2021-05-06 05:54:18] * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 05:54:18] * Making basecall !!
INFO [2021-05-06 05:54:19] * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 05:54:19] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:19] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.04 secs
SUCCESS [2021-05-06 05:54:21] >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 05:54:21] ******** Contig Name: Achl_ACHLO040-09
INFO [2021-05-06 05:54:21] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 05:54:21] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 05:54:21] * Creating Forward Read raw abif ...
INFO [2021-05-06 05:54:21] * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 05:54:21] * Making basecall !!
INFO [2021-05-06 05:54:22] * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 05:54:22] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:22] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 05:54:22] * Creating Reverse Read raw abif ...
INFO [2021-05-06 05:54:22] * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 05:54:22] * Making basecall !!
INFO [2021-05-06 05:54:22] * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 05:54:23] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:23] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.04 secs
SUCCESS [2021-05-06 05:54:25] >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 05:54:25] ******** Contig Name: Achl_ACHLO041-09
INFO [2021-05-06 05:54:25] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 05:54:25] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 05:54:25] * Creating Forward Read raw abif ...
INFO [2021-05-06 05:54:25] * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 05:54:25] * Making basecall !!
INFO [2021-05-06 05:54:25] * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 05:54:26] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:26] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 05:54:26] * Creating Reverse Read raw abif ...
INFO [2021-05-06 05:54:26] * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 05:54:26] * Making basecall !!
INFO [2021-05-06 05:54:26] * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 05:54:26] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:26] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.05 secs
SUCCESS [2021-05-06 05:54:28] >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 05:54:28] Aligning consensus reads ...
SUCCESS [2021-05-06 05:54:29] >> 'SangerAlignment' S4 instance is created !!
INFO [2021-05-06 05:54:29] *************************************************
INFO [2021-05-06 05:54:29] **** Start creating SangerAlignment instance ****
INFO [2021-05-06 05:54:30] *************************************************
INFO [2021-05-06 05:54:30] **** You are using CSV Name Conversion Method to group reads in FASTA file (with CSV file)!
INFO [2021-05-06 05:54:30] ******** Contig Name: Achl_ACHLO006-09
INFO [2021-05-06 05:54:30] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 05:54:30] **** Your contig name is Achl_ACHLO006-09
INFO [2021-05-06 05:54:30] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 05:54:30] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:30] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 05:54:30] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:30] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.04 secs
SUCCESS [2021-05-06 05:54:32] >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 05:54:32] ******** Contig Name: Achl_ACHLO007-09
INFO [2021-05-06 05:54:32] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 05:54:32] **** Your contig name is Achl_ACHLO007-09
INFO [2021-05-06 05:54:32] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 05:54:33] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:33] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 05:54:33] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:33] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.06 secs
SUCCESS [2021-05-06 05:54:35] >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 05:54:35] ******** Contig Name: Achl_ACHLO040-09
INFO [2021-05-06 05:54:35] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 05:54:35] **** Your contig name is Achl_ACHLO040-09
INFO [2021-05-06 05:54:35] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 05:54:36] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:36] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 05:54:36] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:36] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.05 secs
SUCCESS [2021-05-06 05:54:38] >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 05:54:38] ******** Contig Name: Achl_ACHLO041-09
INFO [2021-05-06 05:54:38] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 05:54:38] **** Your contig name is Achl_ACHLO041-09
INFO [2021-05-06 05:54:38] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 05:54:38] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:38] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 05:54:39] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:39] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.05 secs
SUCCESS [2021-05-06 05:54:41] >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 05:54:41] Aligning consensus reads ...
SUCCESS [2021-05-06 05:54:42] >> 'SangerAlignment' S4 instance is created !!
INFO [2021-05-06 05:54:42] ******** Contig Name: Achl_ACHLO006-09
INFO [2021-05-06 05:54:42] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 05:54:42] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 05:54:42] * Creating Forward Read raw abif ...
INFO [2021-05-06 05:54:42] * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 05:54:42] * Making basecall !!
INFO [2021-05-06 05:54:42] * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 05:54:43] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:43] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 05:54:43] * Creating Reverse Read raw abif ...
INFO [2021-05-06 05:54:43] * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 05:54:43] * Making basecall !!
INFO [2021-05-06 05:54:43] * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 05:54:44] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:44] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.04 secs
SUCCESS [2021-05-06 05:54:46] >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 05:54:46] ******** Contig Name: Achl_RBNII384-13
INFO [2021-05-06 05:54:46] **** You are using Regular Expression Method to group AB1 files!
INFO [2021-05-06 05:54:46] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 05:54:46] * Creating Forward Read raw abif ...
INFO [2021-05-06 05:54:46] * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 05:54:46] * Making basecall !!
INFO [2021-05-06 05:54:46] * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 05:54:46] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:46] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 05:54:46] * Creating Reverse Read raw abif ...
INFO [2021-05-06 05:54:46] * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 05:54:46] * Making basecall !!
INFO [2021-05-06 05:54:47] * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 05:54:47] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:47] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.06 secs
SUCCESS [2021-05-06 05:54:49] >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 05:54:49] ******** Contig Name: Achl_ACHLO006-09
INFO [2021-05-06 05:54:49] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 05:54:49] **** Your contig name is Achl_ACHLO006-09
INFO [2021-05-06 05:54:49] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 05:54:49] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:49] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 05:54:50] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:50] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.09 secs
SUCCESS [2021-05-06 05:54:51] >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 05:54:52] ******** Contig Name: Achl_RBNII384-13
INFO [2021-05-06 05:54:52] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2021-05-06 05:54:52] **** Your contig name is Achl_RBNII384-13
INFO [2021-05-06 05:54:52] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 05:54:52] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:52] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 05:54:52] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:52] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.05 secs
SUCCESS [2021-05-06 05:54:54] >> 'SangerContig' S4 instance is created !!
INFO [2021-05-06 05:54:54] Forward Read: Creating abif & sangerseq ...
INFO [2021-05-06 05:54:54] * Creating Forward Read raw abif ...
INFO [2021-05-06 05:54:54] * Creating Forward Read raw sangerseq ...
INFO [2021-05-06 05:54:54] * Making basecall !!
INFO [2021-05-06 05:54:55] * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 05:54:55] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:55] Reverse Read: Creating abif & sangerseq ...
INFO [2021-05-06 05:54:55] * Creating Reverse Read raw abif ...
INFO [2021-05-06 05:54:55] * Creating Reverse Read raw sangerseq ...
INFO [2021-05-06 05:54:55] * Making basecall !!
INFO [2021-05-06 05:54:55] * Updating slots in 'SangerRead' instance !!
SUCCESS [2021-05-06 05:54:56] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:56] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 05:54:56] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:56] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2021-05-06 05:54:56] >> 'SangerRead' S4 instance is created !!
INFO [2021-05-06 05:54:57] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.06 secs
INFO [2021-05-06 05:55:00] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.05 secs
INFO [2021-05-06 05:55:02] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.05 secs
INFO [2021-05-06 05:55:05] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.04 secs
INFO [2021-05-06 05:55:07] Aligning consensus reads ...
INFO [2021-05-06 05:55:09] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.05 secs
INFO [2021-05-06 05:55:11] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.04 secs
INFO [2021-05-06 05:55:14] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.05 secs
INFO [2021-05-06 05:55:17] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.05 secs
INFO [2021-05-06 05:55:19] Aligning consensus reads ...
INFO [2021-05-06 05:55:21] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.05 secs
INFO [2021-05-06 05:55:24] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.05 secs
INFO [2021-05-06 05:55:26] * Making basecall !!
INFO [2021-05-06 05:55:27] * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 05:55:27] * Making basecall !!
INFO [2021-05-06 05:55:27] * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 05:55:28] * Making basecall !!
INFO [2021-05-06 05:55:28] * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 05:55:28] * Making basecall !!
INFO [2021-05-06 05:55:29] * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 05:55:29] * Making basecall !!
INFO [2021-05-06 05:55:29] * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 05:55:33] >>> outputDir : /tmp/RtmptIADxW
INFO [2021-05-06 05:55:33] Start writing '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/sangeranalyseR/extdata//Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1' to FASTA format ...
INFO [2021-05-06 05:55:33] >> '/tmp/RtmptIADxW/Achl_ACHLO006-09_1_F.fa' is written
INFO [2021-05-06 05:55:34] >>> outputDir : /tmp/RtmptIADxW
INFO [2021-05-06 05:55:34] Start writing '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/sangeranalyseR/extdata//fasta/SangerRead/Achl_ACHLO006-09_1_F.fa' to FASTA format ...
INFO [2021-05-06 05:55:34] >> '/tmp/RtmptIADxW/Achl_ACHLO006-09_1_F.fa' is written
INFO [2021-05-06 05:55:34] >>> outputDir : /tmp/RtmptIADxW
INFO [2021-05-06 05:55:34] Start writing '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/sangeranalyseR/extdata//fasta/SangerRead/Achl_ACHLO006-09_2_R.fa' to FASTA format ...
INFO [2021-05-06 05:55:34] >> '/tmp/RtmptIADxW/Achl_ACHLO006-09_2_R.fa' is written
INFO [2021-05-06 05:55:34] Aligning consensus reads ...
INFO [2021-05-06 05:55:35] Correcting frameshifts in reads using amino acidreference sequence
Assessing frameshifts in nucleotide sequences:
================================================================================
Time difference of 0.04 secs
INFO [2021-05-06 05:55:37] * Making basecall !!
INFO [2021-05-06 05:55:37] * Updating slots in 'SangerRead' instance !!
INFO [2021-05-06 05:55:37] * Making basecall !!
INFO [2021-05-06 05:55:37] * Updating slots in 'SangerRead' instance !!
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 930 ]
>
> proc.time()
user system elapsed
92.768 1.520 94.548
Example timings
sangeranalyseR.Rcheck/sangeranalyseR-Ex.timings