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This page was generated on 2022-10-19 13:20:25 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 nebbiolo1


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 974/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IONiseR 2.20.0  (landing page)
Mike Smith
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/IONiseR
git_branch: RELEASE_3_15
git_last_commit: 6519986
git_last_commit_date: 2022-04-26 11:25:57 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: IONiseR
Version: 2.20.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:IONiseR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings IONiseR_2.20.0.tar.gz
StartedAt: 2022-10-18 20:14:07 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 20:18:01 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 234.5 seconds
RetCode: 0
Status:   OK  
CheckDir: IONiseR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:IONiseR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings IONiseR_2.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/IONiseR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IONiseR/DESCRIPTION’ ... OK
* this is package ‘IONiseR’ version ‘2.20.0’
* 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 8.049  0.415   8.465
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/IONiseR.Rcheck/00check.log’
for details.



Installation output

IONiseR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL IONiseR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 15.552   0.797  16.339 

Example timings

IONiseR.Rcheck/IONiseR-Ex.timings

nameusersystemelapsed
Fast5Summary-class2.2600.1762.439
baseCalled1.2620.0601.322
channelActivityPlot2.0040.1432.150
channelHeatmap0.7220.0590.782
eventData0.5410.0330.573
fast5toFastq0.0000.0000.001
fastq0.5060.0520.558
fastq2D1.4250.0791.504
fastqComplement0.5110.0040.515
fastqTemplate0.5070.0200.528
layoutPlot0.6790.0440.722
plotActiveChannels0.6790.0520.731
plotBaseProductionRate1.6090.0891.697
plotCurrentByTime0.7220.0380.761
plotEventRate0.7270.0400.767
plotKmerFrequencyCorrelation8.0490.4158.465
plotReadAccumulation0.6500.0160.666
plotReadCategoryCounts0.6710.0560.728
plotReadCategoryQuals1.6730.0251.697
plotReadTypeProduction0.6450.0310.676
readFast5Log0.0060.0010.007
readFast5Summary000
readInfo0.5050.0150.520