BioC 3.4: CHECK report for IONiseR on morelia

Package: IONiseR

Version: 1.4.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IONiseR_1.4.4.tar.gz

StartedAt: 2017-04-15 03:55:24 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 03:58:57 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 212.8 seconds

RetCode: 0

Status:  OK

CheckDir: IONiseR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IONiseR_1.4.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/IONiseR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IONiseR/DESCRIPTION’ ... OK
* this is package ‘IONiseR’ version ‘1.4.4’
* 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 ... OK
* 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 ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       3.9Mb
    extdata   1.5Mb
* 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 loading without being on the library search path ... 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
.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 binding for global variable ‘matrixRow’
.processFastq: no visible binding for global variable ‘readIDs’
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 ‘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 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 ‘accumulation’
plotActiveChannels: no visible binding for global variable ‘start_time’
plotActiveChannels: no visible binding for global variable ‘duration’
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
  ‘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’
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’
readFast5Summary2: no visible binding for global variable ‘num_events’
readFast5Summary2: no visible binding for global variable ‘start_time’
readFast5Summary3: no visible binding for global variable ‘num_events’
readFast5Summary3: no visible binding for global variable ‘start_time’
readFast5SummaryTar: no visible binding for global variable
  ‘num_events’
readFast5SummaryTar: no visible binding for global variable
  ‘start_time’
[,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 idx matrixCol matrixRow meanZValue mean_value median_signal
  mux nbases new_reads num_events oddEven pass pentamer readIDs
  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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
plotKmerFrequencyCorrelation 5.088  0.592   5.814
channelActivityPlot          1.947  0.080   5.477
* 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-3.4-bioc/meat/IONiseR.Rcheck/00check.log’
for details.

* installing *source* package ‘IONiseR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IONiseR)

name	user	system	elapsed
Fast5Summary-class	1.418	0.053	2.484
baseCalled	0.803	0.025	0.829
channelActivityPlot	1.947	0.080	5.477
channelHeatmap	1.517	0.040	1.598
fastq	0.828	0.057	0.886
fastq2D	0.491	0.013	0.505
fastqComplement	0.464	0.024	0.489
fastqTemplate	0.522	0.027	0.549
layoutPlot	1.161	0.038	1.236
plotActiveChannels	0.624	0.032	0.724
plotBaseProductionRate	0.962	0.031	1.009
plotCurrentByTime	0.766	0.023	0.835
plotEventRate	1.182	0.060	1.273
plotKmerFrequencyCorrelation	5.088	0.592	5.814
plotReadAccumulation	0.774	0.066	1.006
plotReadCategoryCounts	0.647	0.055	0.754
plotReadCategoryQuals	0.872	0.072	0.960
plotReadTypeProduction	0.638	0.014	0.659
rawData	0.399	0.013	0.412
readFast5Summary	0.001	0.000	0.000
readInfo	0.438	0.035	0.474