Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1045/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
IONiseR 2.30.0 (landing page) Mike Smith
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the IONiseR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IONiseR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: IONiseR |
Version: 2.30.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IONiseR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IONiseR_2.30.0.tar.gz |
StartedAt: 2024-12-20 04:56:33 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:05:31 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 537.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: IONiseR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IONiseR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IONiseR_2.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/IONiseR.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘IONiseR/DESCRIPTION’ ... OK * this is package ‘IONiseR’ version ‘2.30.0’ * 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 code 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 (user + system) or elapsed time > 5s user system elapsed plotKmerFrequencyCorrelation 16.411 0.815 19.307 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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-3.20-bioc/meat/IONiseR.Rcheck/00check.log’ for details.
IONiseR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL IONiseR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘IONiseR’ ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (IONiseR)
IONiseR.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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") [ FAIL 0 | WARN 18 | SKIP 0 | PASS 24 ] [ FAIL 0 | WARN 18 | SKIP 0 | PASS 24 ] > > proc.time() user system elapsed 31.634 1.639 37.267
IONiseR.Rcheck/IONiseR-Ex.timings
name | user | system | elapsed | |
Fast5Summary-class | 1.482 | 0.100 | 1.920 | |
baseCalled | 1.449 | 0.043 | 1.832 | |
channelActivityPlot | 2.630 | 0.156 | 3.196 | |
channelHeatmap | 1.157 | 0.049 | 1.350 | |
eventData | 0.653 | 0.038 | 0.773 | |
fast5toFastq | 0.001 | 0.001 | 0.001 | |
fastq | 0.625 | 0.037 | 0.731 | |
fastq2D | 1.481 | 0.045 | 1.654 | |
fastqComplement | 0.628 | 0.051 | 0.740 | |
fastqTemplate | 0.630 | 0.055 | 0.738 | |
layoutPlot | 1.100 | 0.037 | 1.227 | |
plotActiveChannels | 1.753 | 0.044 | 1.963 | |
plotBaseProductionRate | 1.052 | 0.040 | 1.205 | |
plotCurrentByTime | 1.827 | 0.049 | 2.035 | |
plotEventRate | 1.029 | 0.070 | 1.181 | |
plotKmerFrequencyCorrelation | 16.411 | 0.815 | 19.307 | |
plotReadAccumulation | 0.879 | 0.056 | 1.055 | |
plotReadCategoryCounts | 1.022 | 0.053 | 1.235 | |
plotReadCategoryQuals | 1.309 | 0.068 | 1.644 | |
plotReadTypeProduction | 1.791 | 0.103 | 2.099 | |
readFast5Log | 0.009 | 0.002 | 0.016 | |
readFast5Summary | 0.000 | 0.001 | 0.000 | |
readInfo | 0.628 | 0.038 | 0.746 | |