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CHECK report for IONiseR on celaya2

This page was generated on 2019-04-09 13:14:21 -0400 (Tue, 09 Apr 2019).

Package 812/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IONiseR 2.7.0
Mike Smith
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/IONiseR
Branch: master
Last Commit: 377512a
Last Changed Date: 2018-10-30 11:54:34 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: IONiseR
Version: 2.7.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IONiseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IONiseR_2.7.0.tar.gz
StartedAt: 2019-04-09 02:54:44 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:59:55 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 311.3 seconds
RetCode: 0
Status:  OK 
CheckDir: IONiseR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IONiseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IONiseR_2.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/IONiseR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IONiseR/DESCRIPTION’ ... OK
* this is package ‘IONiseR’ version ‘2.7.0’
* 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 or elapsed time > 5s
                             user system elapsed
plotKmerFrequencyCorrelation 7.07  0.632   7.702
* 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-3.9-bioc/meat/IONiseR.Rcheck/00check.log’
for details.



Installation output

IONiseR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL IONiseR
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 39 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 17.987   1.454  19.414 

Example timings

IONiseR.Rcheck/IONiseR-Ex.timings

nameusersystemelapsed
Fast5Summary-class1.8630.1171.988
baseCalled1.6100.1051.715
channelActivityPlot2.0330.1782.217
channelHeatmap0.9280.0510.980
eventData0.6620.0770.740
fast5toFastq0.0000.0000.001
fastq0.5760.0560.631
fastq2D1.3210.0671.388
fastqComplement0.5340.0420.576
fastqTemplate0.5740.0620.636
layoutPlot0.8010.0400.841
plotActiveChannels1.5140.0641.579
plotBaseProductionRate0.8020.0640.866
plotCurrentByTime1.5210.0441.566
plotEventRate0.7310.0520.783
plotKmerFrequencyCorrelation7.0700.6327.702
plotReadAccumulation0.6710.1030.775
plotReadCategoryCounts0.6780.1070.785
plotReadCategoryQuals1.1010.1921.294
plotReadTypeProduction0.7950.0550.851
readFast5Log0.0060.0020.010
readFast5Summary0.0000.0010.001
readInfo0.5220.0250.547