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This page was generated on 2022-04-13 12:08:12 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for IONiseR on machv2


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

raw results

Package 949/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IONiseR 2.18.0  (landing page)
Mike Smith
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/IONiseR
git_branch: RELEASE_3_14
git_last_commit: 9256877
git_last_commit_date: 2021-10-26 12:21:10 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: IONiseR
Version: 2.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IONiseR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IONiseR_2.18.0.tar.gz
StartedAt: 2022-04-12 14:33:10 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 14:38:50 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 340.8 seconds
RetCode: 0
Status:   OK  
CheckDir: IONiseR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IONiseR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IONiseR_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/IONiseR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IONiseR/DESCRIPTION’ ... OK
* this is package ‘IONiseR’ version ‘2.18.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
plotKmerFrequencyCorrelation 11.297   0.62  11.942
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/IONiseR.Rcheck/00check.log’
for details.



Installation output

IONiseR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL IONiseR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘IONiseR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (IONiseR)

Tests output

IONiseR.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(IONiseR)
> 
> test_check("IONiseR")
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 24 ]

[ FAIL 0 | WARN 18 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
 22.837   1.069  23.906 

Example timings

IONiseR.Rcheck/IONiseR-Ex.timings

nameusersystemelapsed
Fast5Summary-class1.2210.0721.301
baseCalled1.3020.0321.335
channelActivityPlot1.9700.1212.093
channelHeatmap1.7000.0341.735
eventData1.3060.0701.376
fast5toFastq0.0000.0000.001
fastq0.5590.0200.580
fastq2D0.6050.0310.636
fastqComplement0.6100.0360.647
fastqTemplate0.5990.0310.631
layoutPlot0.9320.0460.981
plotActiveChannels0.8400.0440.887
plotBaseProductionRate0.9580.0361.007
plotCurrentByTime1.6130.0461.677
plotEventRate0.8100.0310.842
plotKmerFrequencyCorrelation11.297 0.62011.942
plotReadAccumulation0.7370.0270.766
plotReadCategoryCounts1.5970.0571.656
plotReadCategoryQuals0.9320.0270.960
plotReadTypeProduction0.8610.0370.899
readFast5Log0.0080.0010.009
readFast5Summary0.0000.0000.001
readInfo0.5870.0470.633