Joseph R Boyd
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/seqsetvis |
| Branch: master |
| Last Commit: 4c7e98e |
| Last Changed Date: 2019-02-21 00:00:54 -0400 (Thu, 21 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:20:08 -0400 (Tue, 09 Apr 2019).
| Package 1469/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| seqsetvis 1.3.6 Joseph R Boyd
| 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: seqsetvis |
| Version: 1.3.6 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings seqsetvis_1.3.6.tar.gz |
| StartedAt: 2019-04-09 05:25:59 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:35:17 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 558.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: seqsetvis.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings seqsetvis_1.3.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/seqsetvis.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqsetvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqsetvis’ version ‘1.3.6’
* package encoding: UTF-8
* 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 ‘seqsetvis’ 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
ssvFetchBam.single: no visible binding for global variable ‘x’
ssvFetchBam.single: no visible binding for global variable ‘id’
Undefined global functions or variables:
id x
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ssvFetchBam 18.633 5.944 10.414
ssvSignalBandedQuantiles 14.825 4.958 10.607
ssvFetchSignal 6.588 1.945 2.359
ssvSignalClustering 6.000 2.340 3.317
ssvFetchBigwig 5.569 2.198 1.729
fragLen_calcStranded 5.551 0.786 3.809
ssvFetchGRanges 3.906 2.300 1.004
ssvSignalScatterplot 3.895 2.165 1.733
ssvSignalLineplotAgg 3.944 1.868 2.155
ssvSignalLineplot 5.182 0.590 4.711
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/seqsetvis.Rcheck/00check.log’
for details.
seqsetvis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL seqsetvis ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘seqsetvis’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (seqsetvis)
seqsetvis.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" 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. > > ## load dependencies > library(testthat) > library(seqsetvis) Loading required package: ggplot2 > library(data.table) > > ## test package > test_check(package = "seqsetvis") ══ testthat results ═══════════════════════════════════════════════════════════ OK: 988 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 455.612 200.752 193.214
seqsetvis.Rcheck/seqsetvis-Ex.timings
| name | user | system | elapsed | |
| applySpline | 3.299 | 1.542 | 1.969 | |
| centerAtMax | 1.751 | 1.049 | 0.602 | |
| centerFixedSizeGRanges | 0.608 | 0.318 | 0.378 | |
| clusteringKmeans | 0.151 | 0.095 | 0.078 | |
| clusteringKmeansNestedHclust | 0.176 | 0.120 | 0.062 | |
| col2hex | 0.008 | 0.005 | 0.004 | |
| crossCorrByRle | 1.062 | 0.327 | 0.793 | |
| easyLoad_bed | 0.087 | 0.002 | 0.089 | |
| easyLoad_broadPeak | 0.220 | 0.001 | 0.223 | |
| easyLoad_narrowPeak | 0.056 | 0.001 | 0.057 | |
| fragLen_calcStranded | 5.551 | 0.786 | 3.809 | |
| fragLen_fromMacs2Xls | 0.003 | 0.001 | 0.004 | |
| ggellipse | 1.066 | 0.016 | 1.082 | |
| harmonize_seqlengths | 0.185 | 0.010 | 0.195 | |
| prepare_fetch_GRanges | 0.027 | 0.001 | 0.028 | |
| quantileGRangesWidth | 0.001 | 0.000 | 0.001 | |
| safeBrew | 0.038 | 0.003 | 0.042 | |
| ssvFactorizeMembTable | 0.041 | 0.003 | 0.045 | |
| ssvFeatureBars | 1.679 | 0.034 | 1.714 | |
| ssvFeatureBinaryHeatmap | 0.815 | 0.005 | 0.823 | |
| ssvFeatureEuler | 0.994 | 0.011 | 1.023 | |
| ssvFeaturePie | 1.010 | 0.004 | 1.015 | |
| ssvFeatureVenn | 1.089 | 0.013 | 1.102 | |
| ssvFetchBam | 18.633 | 5.944 | 10.414 | |
| ssvFetchBigwig | 5.569 | 2.198 | 1.729 | |
| ssvFetchGRanges | 3.906 | 2.300 | 1.004 | |
| ssvFetchSignal | 6.588 | 1.945 | 2.359 | |
| ssvMakeMembTable-methods | 1.193 | 0.334 | 0.902 | |
| ssvOverlapIntervalSets | 0.436 | 0.008 | 0.445 | |
| ssvSignalBandedQuantiles | 14.825 | 4.958 | 10.607 | |
| ssvSignalClustering | 6.000 | 2.340 | 3.317 | |
| ssvSignalHeatmap | 3.623 | 1.317 | 1.985 | |
| ssvSignalLineplot | 5.182 | 0.590 | 4.711 | |
| ssvSignalLineplotAgg | 3.944 | 1.868 | 2.155 | |
| ssvSignalScatterplot | 3.895 | 2.165 | 1.733 | |
| viewGRangesWinSample_dt | 2.886 | 0.898 | 2.042 | |
| viewGRangesWinSummary_dt | 2.939 | 1.349 | 1.558 | |