Package: IONiseR

Version: 2.6.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IONiseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings IONiseR_2.6.0.tar.gz

StartedAt: 2019-04-13 03:13:39 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 03:19:30 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 351.4 seconds

RetCode: 0

Status:  OK

CheckDir: IONiseR.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IONiseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings IONiseR_2.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/IONiseR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IONiseR/DESCRIPTION' ... OK
* this is package 'IONiseR' version '2.6.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/IONiseR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/IONiseR_2.6.0.tar.gz && rm -rf IONiseR.buildbin-libdir && mkdir IONiseR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IONiseR.buildbin-libdir IONiseR_2.6.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL IONiseR_2.6.0.zip && rm IONiseR_2.6.0.tar.gz IONiseR_2.6.0.zip
###
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install for i386

* installing *source* package 'IONiseR' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'IONiseR'
    finding HTML links ... done
    Fast5Summary-class                      html  
    IONiseR                                 html  
    baseCalled                              html  
    channelActivityPlot                     html  
    channelHeatmap                          html  
    eventData                               html  
    fast5toFastq                            html  
    fastq                                   html  
    fastq2D                                 html  
    fastqComplement                         html  
    fastqTemplate                           html  
    layoutPlot                              html  
    muxHeatmap                              html  
    plotActiveChannels                      html  
    plotBaseProductionRate                  html  
    plotCurrentByTime                       html  
    plotEventRate                           html  
    plotKmerFrequencyCorrelation            html  
    plotReadAccumulation                    html  
    plotReadCategoryCounts                  html  
    plotReadCategoryQuals                   html  
    plotReadTypeProduction                  html  
    readFast5Log                            html  
    readFast5Summary                        html  
    readInfo                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'IONiseR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IONiseR' as IONiseR_2.6.0.zip
* DONE (IONiseR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'IONiseR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  10.53    0.79   11.57 

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  12.31    0.40   12.71