Mike Smith
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/IONiseR |
| Branch: RELEASE_3_8 |
| Last Commit: 9690b6b |
| Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:58:47 -0400 (Tue, 16 Apr 2019).
| Package 788/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IONiseR 2.6.0 Mike Smith
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: IONiseR |
| Version: 2.6.0 |
| 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_2.6.0.tar.gz |
| StartedAt: 2019-04-16 00:44:01 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 00:47:51 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 230.7 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_2.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/IONiseR.Rcheck’ * using R version 3.5.3 (2019-03-11) * 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 ‘2.6.0’ * 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 * 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-3.8-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/3.5/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 version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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
14.243 0.725 15.034
IONiseR.Rcheck/IONiseR-Ex.timings
| name | user | system | elapsed | |
| Fast5Summary-class | 1.541 | 0.063 | 1.615 | |
| baseCalled | 1.101 | 0.039 | 1.143 | |
| channelActivityPlot | 1.519 | 0.094 | 1.624 | |
| channelHeatmap | 0.805 | 0.025 | 0.837 | |
| eventData | 0.624 | 0.046 | 0.676 | |
| fast5toFastq | 0.000 | 0.000 | 0.001 | |
| fastq | 0.446 | 0.015 | 0.462 | |
| fastq2D | 0.978 | 0.036 | 1.018 | |
| fastqComplement | 0.459 | 0.018 | 0.479 | |
| fastqTemplate | 0.492 | 0.037 | 0.535 | |
| layoutPlot | 0.723 | 0.021 | 0.754 | |
| plotActiveChannels | 1.154 | 0.031 | 1.188 | |
| plotBaseProductionRate | 0.688 | 0.032 | 0.723 | |
| plotCurrentByTime | 1.219 | 0.027 | 1.256 | |
| plotEventRate | 0.587 | 0.025 | 0.615 | |
| plotKmerFrequencyCorrelation | 4.106 | 0.363 | 4.491 | |
| plotReadAccumulation | 0.653 | 0.057 | 0.712 | |
| plotReadCategoryCounts | 0.612 | 0.054 | 0.669 | |
| plotReadCategoryQuals | 0.927 | 0.033 | 0.964 | |
| plotReadTypeProduction | 1.315 | 0.075 | 1.396 | |
| readFast5Log | 0.005 | 0.001 | 0.007 | |
| readFast5Summary | 0.000 | 0.000 | 0.001 | |
| readInfo | 0.580 | 0.049 | 0.638 | |