Package: IONiseR

Version: 2.7.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IONiseR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IONiseR_2.7.0.tar.gz

StartedAt: 2019-04-09 01:25:26 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:29:11 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 224.6 seconds

RetCode: 0

Status:  OK

CheckDir: IONiseR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IONiseR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IONiseR_2.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/IONiseR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.7.0’
* 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 4.913  0.092   5.006
* 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-3.9-bioc/meat/IONiseR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL IONiseR
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* installing to library ‘/home/biocbuild/bbs-3.9-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)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 39 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 12.639   0.458  13.345 

name	user	system	elapsed
Fast5Summary-class	1.078	0.040	1.185
baseCalled	1.127	0.036	1.162
channelActivityPlot	2.042	0.104	2.761
channelHeatmap	1.047	0.028	1.075
eventData	0.747	0.016	0.762
fast5toFastq	0	0	0
fastq	0.674	0.024	0.698
fastq2D	1.190	0.012	1.203
fastqComplement	0.551	0.012	0.563
fastqTemplate	0.685	0.012	0.697
layoutPlot	0.827	0.008	0.835
plotActiveChannels	1.420	0.008	1.429
plotBaseProductionRate	0.681	0.012	0.693
plotCurrentByTime	1.316	0.000	1.316
plotEventRate	0.755	0.028	0.783
plotKmerFrequencyCorrelation	4.913	0.092	5.006
plotReadAccumulation	0.623	0.008	0.631
plotReadCategoryCounts	0.835	0.020	0.858
plotReadCategoryQuals	1.079	0.028	1.106
plotReadTypeProduction	0.955	0.004	0.958
readFast5Log	0.008	0.000	0.069
readFast5Summary	0.000	0.000	0.001
readInfo	0.776	0.020	0.797