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BioC 3.4: CHECK report for IONiseR on tokay1

This page was generated on 2017-04-15 16:20:05 -0400 (Sat, 15 Apr 2017).

Package 640/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IONiseR 1.4.4
Mike Smith
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/IONiseR
Last Changed Rev: 127019 / Revision: 128728
Last Changed Date: 2017-02-27 22:41:53 -0500 (Mon, 27 Feb 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: IONiseR
Version: 1.4.4
Command: rm -rf IONiseR.buildbin-libdir IONiseR.Rcheck && mkdir IONiseR.buildbin-libdir IONiseR.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IONiseR.buildbin-libdir IONiseR_1.4.4.tar.gz >IONiseR.Rcheck\00install.out 2>&1 && cp IONiseR.Rcheck\00install.out IONiseR-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=IONiseR.buildbin-libdir --install="check:IONiseR-install.out" --force-multiarch --no-vignettes --timings IONiseR_1.4.4.tar.gz
StartedAt: 2017-04-14 23:06:22 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:11:42 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 320.1 seconds
RetCode: 0
Status:  OK  
CheckDir: IONiseR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf IONiseR.buildbin-libdir IONiseR.Rcheck && mkdir IONiseR.buildbin-libdir IONiseR.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IONiseR.buildbin-libdir IONiseR_1.4.4.tar.gz >IONiseR.Rcheck\00install.out 2>&1 && cp IONiseR.Rcheck\00install.out IONiseR-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=IONiseR.buildbin-libdir --install="check:IONiseR-install.out" --force-multiarch --no-vignettes --timings IONiseR_1.4.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/IONiseR.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '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 whether package 'IONiseR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    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
* 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
** checking loading without being on the library search path ... 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plotKmerFrequencyCorrelation 5.19   0.47    5.67
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plotKmerFrequencyCorrelation  5.6   0.28    5.87
* 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-3.4-bioc/meat/IONiseR.Rcheck/00check.log'
for details.


IONiseR.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'IONiseR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IONiseR' as IONiseR_1.4.4.zip
* DONE (IONiseR)

IONiseR.Rcheck/examples_i386/IONiseR-Ex.timings:

nameusersystemelapsed
Fast5Summary-class1.910.002.41
baseCalled0.940.061.00
channelActivityPlot2.180.112.66
channelHeatmap1.490.031.51
fastq0.950.101.05
fastq2D0.850.030.87
fastqComplement0.780.050.83
fastqTemplate0.630.030.65
layoutPlot1.280.061.35
plotActiveChannels1.220.031.25
plotBaseProductionRate1.340.031.37
plotCurrentByTime1.080.111.19
plotEventRate1.390.021.41
plotKmerFrequencyCorrelation5.190.475.67
plotReadAccumulation0.920.040.97
plotReadCategoryCounts0.690.070.75
plotReadCategoryQuals1.080.071.15
plotReadTypeProduction1.070.041.11
rawData0.700.060.76
readFast5Summary000
readInfo0.750.040.80

IONiseR.Rcheck/examples_x64/IONiseR-Ex.timings:

nameusersystemelapsed
Fast5Summary-class1.980.092.08
baseCalled1.050.051.10
channelActivityPlot2.950.083.03
channelHeatmap2.160.062.22
fastq1.110.061.17
fastq2D0.610.080.69
fastqComplement0.670.030.70
fastqTemplate1.240.051.28
layoutPlot0.890.010.91
plotActiveChannels0.890.050.93
plotBaseProductionRate1.190.081.27
plotCurrentByTime0.920.050.96
plotEventRate1.470.061.54
plotKmerFrequencyCorrelation5.600.285.87
plotReadAccumulation0.760.030.80
plotReadCategoryCounts0.730.030.77
plotReadCategoryQuals0.830.060.89
plotReadTypeProduction0.690.080.76
rawData0.470.030.50
readFast5Summary000
readInfo0.500.020.52