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CHECK report for IONiseR on tokay2

This page was generated on 2020-10-17 11:56:53 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE IONiseR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 889/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IONiseR 2.12.0
Mike Smith
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/IONiseR
Branch: RELEASE_3_11
Last Commit: e288533
Last Changed Date: 2020-04-27 14:49:42 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: IONiseR
Version: 2.12.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IONiseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings IONiseR_2.12.0.tar.gz
StartedAt: 2020-10-17 05:15:36 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:26:27 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 651.4 seconds
RetCode: 0
Status:  OK  
CheckDir: IONiseR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IONiseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings IONiseR_2.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/IONiseR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IONiseR/DESCRIPTION' ... OK
* this is package 'IONiseR' version '2.12.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'IONiseR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.fast5status : <anonymous>: no visible binding for global variable
  'group'
.fast5status : <anonymous>: no visible binding for global variable
  'name'
.get2D: no visible binding for global variable 'full_2D'
.muxToXY: no visible binding for global variable 'matrixCol'
.muxToXY: no visible binding for global variable 'mux'
.muxToXY: no visible binding for global variable 'oddEven'
.muxToXY: no visible global function definition for ':='
.muxToXY: no visible binding for global variable 'matrixRow'
.processFastq: no visible binding for global variable 'readIDs'
.strandExistence: no visible binding for global variable 'name'
.strandExistence: no visible binding for global variable 'group'
channelActivityPlot: no visible binding for global variable 'channel'
channelActivityPlot: no visible binding for global variable
  'start_time'
channelActivityPlot: no visible binding for global variable 'duration'
channelActivityPlot: no visible binding for global variable 'zvalue'
channelActivityPlot: no visible binding for global variable 'time_bin'
channelActivityPlot: no visible binding for global variable
  'mean_value'
layoutPlot: no visible binding for global variable 'channel'
layoutPlot: no visible binding for global variable 'seq_length'
layoutPlot: no visible binding for global variable 'median_signal'
layoutPlot: no visible global function definition for 'error'
muxHeatmap: no visible binding for global variable 'channel'
muxHeatmap: no visible binding for global variable 'matrixRow'
muxHeatmap: no visible binding for global variable 'matrixCol'
muxHeatmap: no visible binding for global variable 'meanZValue'
muxHeatmap: no visible global function definition for 'rbindlist'
muxHeatmap: no visible binding for global variable 'circleFun'
muxHeatmap: no visible binding for global variable 'x'
muxHeatmap: no visible binding for global variable 'y'
plot2DYield: no visible binding for global variable 'start_time'
plot2DYield: no visible binding for global variable 'pass'
plot2DYield: no visible binding for global variable 'nbases'
plot2DYield: no visible binding for global variable 'time_group'
plot2DYield: no visible binding for global variable 'hour'
plot2DYield: no visible binding for global variable 'accumulation'
plotActiveChannels: no visible binding for global variable 'start_time'
plotActiveChannels: no visible binding for global variable 'duration'
plotActiveChannels: no visible binding for global variable 'minute'
plotBaseProductionRate: no visible binding for global variable
  'start_time'
plotBaseProductionRate: no visible binding for global variable
  'bases_called'
plotBaseProductionRate: no visible binding for global variable
  'duration'
plotCurrentByTime: no visible binding for global variable 'start_time'
plotCurrentByTime: no visible binding for global variable
  'median_signal'
plotEventRate: no visible binding for global variable 'start_time'
plotEventRate: no visible binding for global variable 'num_events'
plotEventRate: no visible binding for global variable 'duration'
plotKmerFrequencyCorrelation: no visible binding for global variable
  'full_2D'
plotKmerFrequencyCorrelation: no visible binding for global variable
  'start_time'
plotKmerFrequencyCorrelation: no visible binding for global variable
  'AAAAA'
plotKmerFrequencyCorrelation: no visible binding for global variable
  'TTTTT'
plotKmerFrequencyCorrelation: no visible binding for global variable
  'time_group'
plotKmerFrequencyCorrelation: no visible binding for global variable
  'freq'
plotKmerFrequencyCorrelation: no visible binding for global variable
  'pentamer'
plotKmerFrequencyCorrelation: no visible binding for global variable
  'x'
plotKmerFrequencyCorrelation: no visible binding for global variable
  'y'
plotReadAccumulation: no visible binding for global variable
  'start_time'
plotReadAccumulation: no visible binding for global variable 'minute'
plotReadAccumulation: no visible binding for global variable
  'new_reads'
plotReadAccumulation: no visible binding for global variable
  'accumulation'
plotReadCategoryCounts: no visible binding for global variable
  'full_2D'
plotReadCategoryCounts: no visible binding for global variable 'pass'
plotReadCategoryCounts: no visible binding for global variable
  'category'
plotReadTypeProduction: no visible binding for global variable
  'start_time'
plotReadTypeProduction: no visible binding for global variable
  'time_group'
plotReadTypeProduction: no visible binding for global variable
  'full_2D'
plotReadTypeProduction: no visible binding for global variable 'pass'
plotReadTypeProduction: no visible binding for global variable 'hour'
readFast5Summary: no visible binding for global variable 'start_time'
readFast5Summary: no visible binding for global variable 'duration'
readFast5Summary: no visible binding for global variable 'num_events'
readFast5Summary.mc: no visible binding for global variable
  'start_time'
readFast5Summary.mc: no visible binding for global variable 'duration'
readFast5Summary.mc: no visible binding for global variable
  'num_events'
[,Fast5Summary-ANY-ANY-ANY: no visible binding for global variable
  'baseCalledTemplate'
[,Fast5Summary-ANY-ANY-ANY: no visible binding for global variable
  'baseCalledComplement'
[,Fast5Summary-ANY-ANY-ANY: no visible binding for global variable
  'component'
[,Fast5Summary-ANY-ANY-ANY: no visible binding for global variable
  'idx'
show,Fast5Summary: no visible binding for global variable 'full_2D'
show,Fast5Summary: no visible binding for global variable 'pass'
Undefined global functions or variables:
  := AAAAA TTTTT accumulation baseCalledComplement baseCalledTemplate
  bases_called category channel circleFun component duration error freq
  full_2D group hour idx matrixCol matrixRow meanZValue mean_value
  median_signal minute mux name nbases new_reads num_events oddEven
  pass pentamer rbindlist readIDs seq_length start_time time_bin
  time_group x y zvalue
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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
plotKmerFrequencyCorrelation 44.01   1.27   45.28
channelActivityPlot           2.99   0.30   17.47
Fast5Summary-class            1.89   0.03   23.34
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
plotKmerFrequencyCorrelation 42.57   0.51    43.1
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/IONiseR.Rcheck/00check.log'
for details.



Installation output

IONiseR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/IONiseR_2.12.0.tar.gz && rm -rf IONiseR.buildbin-libdir && mkdir IONiseR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IONiseR.buildbin-libdir IONiseR_2.12.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL IONiseR_2.12.0.zip && rm IONiseR_2.12.0.tar.gz IONiseR_2.12.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1154k  100 1154k    0     0  16.4M      0 --:--:-- --:--:-- --:--:-- 18.1M

install for i386

* installing *source* package 'IONiseR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'IONiseR'
    finding HTML links ... done
    Fast5Summary-class                      html  
    IONiseR                                 html  
    baseCalled                              html  
    channelActivityPlot                     html  
    channelHeatmap                          html  
    eventData                               html  
    fast5toFastq                            html  
    fastq                                   html  
    fastq2D                                 html  
    fastqComplement                         html  
    fastqTemplate                           html  
    layoutPlot                              html  
    muxHeatmap                              html  
    plotActiveChannels                      html  
    plotBaseProductionRate                  html  
    plotCurrentByTime                       html  
    plotEventRate                           html  
    plotKmerFrequencyCorrelation            html  
    plotReadAccumulation                    html  
    plotReadCategoryCounts                  html  
    plotReadCategoryQuals                   html  
    plotReadTypeProduction                  html  
    readFast5Log                            html  
    readFast5Summary                        html  
    readInfo                                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 'IONiseR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IONiseR' as IONiseR_2.12.0.zip
* DONE (IONiseR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'IONiseR' successfully unpacked and MD5 sums checked

Tests output

IONiseR.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(IONiseR)
> 
> test_check("IONiseR")
== testthat results  ===========================================================
[ OK: 24 | SKIPPED: 0 | WARNINGS: 18 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  27.79    2.18   30.31 

IONiseR.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(IONiseR)
> 
> test_check("IONiseR")
== testthat results  ===========================================================
[ OK: 24 | SKIPPED: 0 | WARNINGS: 18 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  26.68    0.82   27.54 

Example timings

IONiseR.Rcheck/examples_i386/IONiseR-Ex.timings

nameusersystemelapsed
Fast5Summary-class 1.89 0.0323.34
baseCalled1.780.001.78
channelActivityPlot 2.99 0.3017.47
channelHeatmap1.610.071.69
eventData1.440.131.56
fast5toFastq000
fastq0.690.030.72
fastq2D0.610.020.62
fastqComplement0.600.070.67
fastqTemplate1.090.041.13
layoutPlot0.750.010.76
plotActiveChannels0.880.030.91
plotBaseProductionRate1.730.051.89
plotCurrentByTime1.190.081.26
plotEventRate1.890.041.94
plotKmerFrequencyCorrelation44.01 1.2745.28
plotReadAccumulation0.920.050.97
plotReadCategoryCounts1.020.001.01
plotReadCategoryQuals1.090.041.14
plotReadTypeProduction1.600.191.78
readFast5Log0.00.00.1
readFast5Summary000
readInfo0.730.090.83

IONiseR.Rcheck/examples_x64/IONiseR-Ex.timings

nameusersystemelapsed
Fast5Summary-class1.210.051.25
baseCalled1.590.081.67
channelActivityPlot2.290.142.44
channelHeatmap1.540.061.59
eventData1.450.031.48
fast5toFastq000
fastq0.610.080.69
fastq2D0.610.050.67
fastqComplement0.830.070.91
fastqTemplate0.730.070.80
layoutPlot0.970.071.04
plotActiveChannels0.800.070.86
plotBaseProductionRate0.920.111.03
plotCurrentByTime1.650.091.75
plotEventRate0.820.050.86
plotKmerFrequencyCorrelation42.57 0.5143.10
plotReadAccumulation0.690.030.72
plotReadCategoryCounts1.010.101.13
plotReadCategoryQuals1.710.111.81
plotReadTypeProduction0.780.090.87
readFast5Log000
readFast5Summary000
readInfo0.480.090.58