Simona Aufiero
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/circRNAprofiler |
| Branch: RELEASE_3_11 |
| Last Commit: 5929d92 |
| Last Changed Date: 2020-06-05 02:50:48 -0400 (Fri, 05 Jun 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:12 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE circRNAprofiler PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 301/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| circRNAprofiler 1.2.1 Simona Aufiero
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: circRNAprofiler |
| Version: 1.2.1 |
| 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_1.2.1.tar.gz |
| StartedAt: 2020-10-16 23:42:30 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 23:59:39 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 1028.5 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_1.2.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/circRNAprofiler.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.2.1’
* 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 44.243 0.138 46.797
annotateRepeats 30.679 2.430 40.035
liftBSJcoords 29.496 2.892 59.158
mergeMotifs 28.394 0.116 29.500
getMotifs 26.620 0.092 28.351
mergeBSJunctions 10.434 0.445 10.955
getMiRsites 7.705 0.132 10.088
getDeseqRes 7.382 0.229 7.635
volcanoPlot 6.484 0.067 6.583
* 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 version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
266.359 5.724 288.047
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
| name | user | system | elapsed | |
| ahChainFiles | 0.241 | 0.007 | 0.305 | |
| ahRepeatMasker | 0.002 | 0.002 | 0.005 | |
| annotateBSJs | 1.002 | 0.022 | 1.092 | |
| annotateRepeats | 30.679 | 2.430 | 40.035 | |
| annotateSNPsGWAS | 1.934 | 0.063 | 2.049 | |
| attractSpecies | 0.001 | 0.002 | 0.004 | |
| backSplicedJunctions | 1.117 | 0.014 | 1.132 | |
| checkProjectFolder | 0.002 | 0.001 | 0.003 | |
| filterCirc | 0.758 | 0.008 | 0.768 | |
| formatGTF | 0.001 | 0.000 | 0.001 | |
| getBackSplicedJunctions | 0.001 | 0.000 | 0.002 | |
| getCircSeqs | 1.297 | 0.029 | 1.328 | |
| getDeseqRes | 7.382 | 0.229 | 7.635 | |
| getDetectionTools | 0.004 | 0.001 | 0.005 | |
| getEdgerRes | 1.183 | 0.013 | 1.204 | |
| getMiRsites | 7.705 | 0.132 | 10.088 | |
| getMotifs | 26.620 | 0.092 | 28.351 | |
| getRandomBSJunctions | 0.245 | 0.005 | 0.250 | |
| getRegexPattern | 0.003 | 0.002 | 0.004 | |
| getSeqsAcrossBSJs | 1.328 | 0.030 | 1.363 | |
| getSeqsFromGRs | 1.503 | 0.040 | 1.617 | |
| gtf | 0.033 | 0.003 | 0.035 | |
| gwasTraits | 0.007 | 0.003 | 0.011 | |
| importCircExplorer2 | 0.031 | 0.002 | 0.034 | |
| importCircMarker | 0.328 | 0.010 | 0.340 | |
| importKnife | 0.040 | 0.003 | 0.043 | |
| importMapSplice | 0.109 | 0.001 | 0.111 | |
| importNCLscan | 0.030 | 0.002 | 0.032 | |
| importOther | 0.023 | 0.002 | 0.025 | |
| importUroborus | 0.029 | 0.002 | 0.031 | |
| initCircRNAprofiler | 0.000 | 0.001 | 0.001 | |
| iupac | 0.002 | 0.002 | 0.004 | |
| liftBSJcoords | 29.496 | 2.892 | 59.158 | |
| memeDB | 0.001 | 0.002 | 0.004 | |
| mergeBSJunctions | 10.434 | 0.445 | 10.955 | |
| mergeMotifs | 28.394 | 0.116 | 29.500 | |
| mergedBSJunctions | 0.701 | 0.006 | 0.709 | |
| miRspeciesCodes | 0.003 | 0.002 | 0.006 | |
| plotExBetweenBSEs | 1.748 | 0.015 | 1.766 | |
| plotExPosition | 1.758 | 0.011 | 1.777 | |
| plotHostGenes | 1.713 | 0.017 | 1.736 | |
| plotLenBSEs | 3.146 | 0.021 | 3.307 | |
| plotLenIntrons | 3.100 | 0.017 | 3.269 | |
| plotMiR | 1.369 | 0.033 | 1.463 | |
| plotMotifs | 44.243 | 0.138 | 46.797 | |
| plotTotExons | 1.740 | 0.015 | 1.845 | |
| rearrangeMiRres | 1.328 | 0.029 | 1.394 | |
| volcanoPlot | 6.484 | 0.067 | 6.583 | |