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This page was generated on 2019-04-09 13:31:44 -0400 (Tue, 09 Apr 2019).
Package 812/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
IONiseR 2.7.0 Mike Smith
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: IONiseR |
Version: 2.7.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IONiseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IONiseR_2.7.0.tar.gz |
StartedAt: 2019-04-09 01:40:50 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 01:45:17 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 266.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: IONiseR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IONiseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IONiseR_2.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/IONiseR.Rcheck’ * using R Under development (unstable) (2018-11-27 r75683) * using platform: x86_64-apple-darwin15.6.0 (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 5.321 0.401 5.757 * 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-3.9-bioc/meat/IONiseR.Rcheck/00check.log’ for details.
IONiseR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL IONiseR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘IONiseR’ ... ** 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 * DONE (IONiseR)
IONiseR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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 15.235 0.784 16.109
IONiseR.Rcheck/IONiseR-Ex.timings
name | user | system | elapsed | |
Fast5Summary-class | 1.637 | 0.069 | 1.720 | |
baseCalled | 1.256 | 0.046 | 1.307 | |
channelActivityPlot | 1.813 | 0.102 | 1.927 | |
channelHeatmap | 0.928 | 0.030 | 0.964 | |
eventData | 0.682 | 0.047 | 0.733 | |
fast5toFastq | 0 | 0 | 0 | |
fastq | 0.558 | 0.030 | 0.592 | |
fastq2D | 1.220 | 0.047 | 1.274 | |
fastqComplement | 0.569 | 0.027 | 0.599 | |
fastqTemplate | 0.566 | 0.039 | 0.609 | |
layoutPlot | 0.794 | 0.032 | 0.845 | |
plotActiveChannels | 1.347 | 0.053 | 1.416 | |
plotBaseProductionRate | 0.770 | 0.049 | 0.858 | |
plotCurrentByTime | 1.393 | 0.045 | 1.449 | |
plotEventRate | 0.750 | 0.041 | 0.796 | |
plotKmerFrequencyCorrelation | 5.321 | 0.401 | 5.757 | |
plotReadAccumulation | 0.656 | 0.061 | 0.721 | |
plotReadCategoryCounts | 0.691 | 0.063 | 0.757 | |
plotReadCategoryQuals | 0.935 | 0.037 | 0.977 | |
plotReadTypeProduction | 1.353 | 0.067 | 1.433 | |
readFast5Log | 0.005 | 0.001 | 0.007 | |
readFast5Summary | 0.000 | 0.000 | 0.001 | |
readInfo | 0.570 | 0.031 | 0.602 | |