Mike Smith
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/IONiseR |
| Branch: RELEASE_3_7 |
| Last Commit: e295684 |
| Last Changed Date: 2018-04-30 10:35:37 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:27:46 -0400 (Wed, 17 Oct 2018).
| Package 746/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IONiseR 2.4.0 Mike Smith
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: IONiseR |
| Version: 2.4.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:IONiseR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings IONiseR_2.4.0.tar.gz |
| StartedAt: 2018-10-16 01:21:47 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 01:24:33 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 166.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IONiseR.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:IONiseR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings IONiseR_2.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/IONiseR.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘IONiseR/DESCRIPTION’ ... OK * this is package ‘IONiseR’ version ‘2.4.0’ * 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 ... 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: 1 NOTE See ‘/home/biocbuild/bbs-3.7-bioc/meat/IONiseR.Rcheck/00check.log’ for details.
IONiseR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL IONiseR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
11.724 0.408 12.257
IONiseR.Rcheck/IONiseR-Ex.timings
| name | user | system | elapsed | |
| Fast5Summary-class | 1.652 | 0.044 | 1.803 | |
| baseCalled | 1.112 | 0.032 | 1.146 | |
| channelActivityPlot | 1.548 | 0.060 | 1.618 | |
| channelHeatmap | 0.808 | 0.032 | 0.843 | |
| eventData | 0.596 | 0.032 | 0.629 | |
| fast5toFastq | 0 | 0 | 0 | |
| fastq | 0.540 | 0.020 | 0.559 | |
| fastq2D | 1.124 | 0.016 | 1.141 | |
| fastqComplement | 0.552 | 0.004 | 0.559 | |
| fastqTemplate | 0.556 | 0.016 | 0.573 | |
| layoutPlot | 0.748 | 0.004 | 0.754 | |
| plotActiveChannels | 1.196 | 0.008 | 1.208 | |
| plotBaseProductionRate | 0.720 | 0.012 | 0.734 | |
| plotCurrentByTime | 1.268 | 0.008 | 1.278 | |
| plotEventRate | 0.708 | 0.012 | 0.722 | |
| plotKmerFrequencyCorrelation | 4.360 | 0.080 | 4.446 | |
| plotReadAccumulation | 0.672 | 0.024 | 0.697 | |
| plotReadCategoryCounts | 0.644 | 0.008 | 0.653 | |
| plotReadCategoryQuals | 0.868 | 0.024 | 0.893 | |
| plotReadTypeProduction | 0.744 | 0.016 | 0.763 | |
| readFast5Log | 0.004 | 0.000 | 0.024 | |
| readFast5Summary | 0.004 | 0.000 | 0.001 | |
| readInfo | 0.596 | 0.000 | 0.595 | |