Simona Aufiero
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/circRNAprofiler |
| Branch: master |
| Last Commit: 1c0450a |
| Last Changed Date: 2019-10-29 13:43:37 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:54:49 -0500 (Thu, 16 Jan 2020).
| Package 293/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| circRNAprofiler 1.1.0 Simona Aufiero
| malbec2 | Linux (Ubuntu 18.04.3 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 | |
| Package: circRNAprofiler |
| Version: 1.1.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings circRNAprofiler_1.1.0.tar.gz |
| StartedAt: 2020-01-16 02:53:53 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 03:09:42 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 949.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: circRNAprofiler.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:circRNAprofiler.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings circRNAprofiler_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/circRNAprofiler.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘circRNAprofiler/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘circRNAprofiler’ version ‘1.1.0’
* 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 ‘circRNAprofiler’ 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 ... OK
* 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 (user + system) or elapsed time > 5s
user system elapsed
plotMotifs 35.258 0.236 37.779
mergeMotifs 24.003 0.278 27.356
getMotifs 21.936 0.217 24.185
getDeseqRes 9.882 0.475 10.469
mergeBSJunctions 9.152 0.327 9.562
volcanoPlot 8.200 0.199 8.690
getMiRsites 7.002 0.196 10.092
* 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: OK
circRNAprofiler.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL circRNAprofiler ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘circRNAprofiler’ ... ** using staged installation ** R ** data ** 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 (circRNAprofiler)
circRNAprofiler.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "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.
> library(testthat)
> library(circRNAprofiler)
Loading required package: gwascat
gwascat loaded. Use makeCurrentGwascat() to extract current image.
from EBI. The data folder of this package has some legacy extracts.
>
> test_check("circRNAprofiler")
trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB
trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB
trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB
trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB
trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 257 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 0 ]
>
> proc.time()
user system elapsed
257.227 14.498 286.392
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
| name | user | system | elapsed | |
| ahChainFiles | 0.260 | 0.013 | 0.273 | |
| ahRepeatMasker | 0.004 | 0.003 | 0.006 | |
| annotateBSJs | 2.085 | 0.026 | 2.393 | |
| annotateRepeats | 2.139 | 0.055 | 2.427 | |
| annotateSNPsGWAS | 2.904 | 0.218 | 3.385 | |
| attractSpecies | 0.002 | 0.002 | 0.005 | |
| backSplicedJunctions | 1.167 | 0.024 | 1.197 | |
| checkProjectFolder | 0.004 | 0.000 | 0.004 | |
| filterCirc | 0.844 | 0.019 | 0.884 | |
| formatGTF | 0.001 | 0.001 | 0.001 | |
| getBackSplicedJunctions | 0.001 | 0.001 | 0.002 | |
| getCircSeqs | 1.554 | 0.042 | 1.606 | |
| getDeseqRes | 9.882 | 0.475 | 10.469 | |
| getDetectionTools | 0.005 | 0.000 | 0.006 | |
| getEdgerRes | 1.214 | 0.048 | 1.266 | |
| getMiRsites | 7.002 | 0.196 | 10.092 | |
| getMotifs | 21.936 | 0.217 | 24.185 | |
| getRandomBSJunctions | 0.092 | 0.006 | 0.100 | |
| getRegexPattern | 0.003 | 0.001 | 0.005 | |
| getSeqsAcrossBSJs | 1.493 | 0.036 | 1.629 | |
| getSeqsFromGRs | 1.652 | 0.042 | 1.794 | |
| gtf | 0.030 | 0.002 | 0.032 | |
| gwasTraits | 0.008 | 0.002 | 0.010 | |
| importCircExplorer2 | 0.022 | 0.002 | 0.039 | |
| importCircMarker | 0.258 | 0.015 | 0.683 | |
| importKnife | 0.033 | 0.003 | 0.036 | |
| importMapSplice | 0.084 | 0.001 | 0.097 | |
| importNCLscan | 0.021 | 0.002 | 0.024 | |
| importOther | 0.023 | 0.002 | 0.026 | |
| importUroborus | 0.020 | 0.002 | 0.023 | |
| initCircRNAprofiler | 0.006 | 0.002 | 0.008 | |
| iupac | 0.003 | 0.001 | 0.003 | |
| liftBSJcoords | 0.751 | 0.013 | 0.765 | |
| mergeBSJunctions | 9.152 | 0.327 | 9.562 | |
| mergeMotifs | 24.003 | 0.278 | 27.356 | |
| mergedBSJunctions | 0.780 | 0.014 | 0.804 | |
| miRspeciesCodes | 0.004 | 0.003 | 0.006 | |
| plotExBetweenBSEs | 1.560 | 0.030 | 1.592 | |
| plotExPosition | 1.524 | 0.020 | 1.547 | |
| plotHostGenes | 1.531 | 0.028 | 1.572 | |
| plotLenBSEs | 2.461 | 0.029 | 2.551 | |
| plotLenIntrons | 2.304 | 0.030 | 2.360 | |
| plotMiR | 1.456 | 0.034 | 1.494 | |
| plotMotifs | 35.258 | 0.236 | 37.779 | |
| plotTotExons | 1.362 | 0.017 | 1.387 | |
| rearrangeMiRres | 1.450 | 0.036 | 1.488 | |
| volcanoPlot | 8.200 | 0.199 | 8.690 | |