IONiseR 1.0.0
Mike Smith
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/IONiseR | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/IONiseR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.0.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IONiseR’ can be installed ... [16s/16s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.channelToXY’ ‘.checkOpening’ ‘.getFastqString’ ‘.getReadChannelMux’
‘.getSamplingRate’ ‘.getSummaryBaseCalled’ ‘.getSummaryRaw’
‘.groupExistsObj’ ‘.idFromFASTQ’ ‘.muxToXY’ ‘.passFailStatus’
‘.processFastqVec’
* 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’
channelHeatmap: no visible binding for global variable ‘channel’
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 global function definition for ‘right_join’
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 global function definition for ‘inner_join’
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’
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
‘full_2D’
plotReadTypeProduction: no visible binding for global variable ‘pass’
plotReadTypeProduction: no visible binding for global variable
‘time_group’
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 : .local: no visible binding for global variable
‘baseCalledTemplate’
[,Fast5Summary-ANY-ANY : .local: no visible binding for global variable
‘baseCalledComplement’
[,Fast5Summary-ANY-ANY : .local: no visible binding for global variable
‘component’
[,Fast5Summary-ANY-ANY : .local: 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’
* 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 ... [31s/35s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotKmerFrequencyCorrelation 5.403 0.474 5.921
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [10s/10s]
[11s/11s] 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-3.2-bioc/meat/IONiseR.Rcheck/00check.log’
for details.
* installing *source* package ‘IONiseR’ ...
** R
** inst
** preparing package for lazy loading
in method for ‘readInfo’ with signature ‘x="Fast5Summary"’: no definition for class “Fast5Summary”
in method for ‘rawData’ with signature ‘x="Fast5Summary"’: no definition for class “Fast5Summary”
in method for ‘baseCalled’ with signature ‘x="Fast5Summary"’: no definition for class “Fast5Summary”
in method for ‘fastq’ with signature ‘x="Fast5Summary"’: no definition for class “Fast5Summary”
in method for ‘[’ with signature ‘"Fast5Summary","ANY"’: no definition for class “Fast5Summary”
in method for ‘fastqTemplate’ with signature ‘x="Fast5Summary"’: no definition for class “Fast5Summary”
in method for ‘fastqComplement’ with signature ‘x="Fast5Summary"’: no definition for class “Fast5Summary”
in method for ‘fastq2D’ with signature ‘x="Fast5Summary"’: no definition for class “Fast5Summary”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IONiseR)