Simona Aufiero
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/circRNAprofiler |
| Branch: RELEASE_3_10 |
| Last Commit: 9167757 |
| Last Changed Date: 2019-10-29 13:11:46 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:49:42 -0400 (Wed, 15 Apr 2020).
| Package 293/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| circRNAprofiler 1.0.0 Simona Aufiero
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: circRNAprofiler |
| Version: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2020-04-15 01:13:06 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:25:18 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 732.0 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_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/circRNAprofiler.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.0.0’
* 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 or elapsed time > 5s
user system elapsed
plotMotifs 31.228 0.128 33.221
mergeMotifs 20.638 0.076 21.663
getMotifs 20.205 0.147 21.850
mergeBSJunctions 6.110 0.168 6.344
getDeseqRes 6.070 0.204 6.321
volcanoPlot 5.763 0.072 5.897
getMiRsites 5.090 0.133 7.574
* 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/3.6/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db
Loading required package: org.Hs.eg.db
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
gwascat loaded. Use data(ebicat38) for hg38 coordinates;
data(ebicat37) for hg19 coordinates.
>
> 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
218.285 8.887 240.509
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
| name | user | system | elapsed | |
| ahChainFiles | 0.253 | 0.008 | 0.263 | |
| ahRepeatMasker | 0.003 | 0.002 | 0.006 | |
| annotateBSJs | 0.758 | 0.015 | 0.783 | |
| annotateRepeats | 1.576 | 0.024 | 1.614 | |
| annotateSNPsGWAS | 2.783 | 0.053 | 2.854 | |
| attractSpecies | 0.002 | 0.002 | 0.004 | |
| backSplicedJunctions | 0.936 | 0.015 | 0.959 | |
| checkProjectFolder | 0.003 | 0.001 | 0.003 | |
| filterCirc | 0.979 | 0.016 | 1.011 | |
| formatGTF | 0.000 | 0.000 | 0.001 | |
| getBackSplicedJunctions | 0.001 | 0.000 | 0.003 | |
| getCircSeqs | 1.002 | 0.029 | 1.044 | |
| getDeseqRes | 6.070 | 0.204 | 6.321 | |
| getDetectionTools | 0.004 | 0.001 | 0.004 | |
| getEdgerRes | 0.976 | 0.030 | 1.015 | |
| getMiRsites | 5.090 | 0.133 | 7.574 | |
| getMotifs | 20.205 | 0.147 | 21.850 | |
| getRandomBSJunctions | 0.071 | 0.004 | 0.077 | |
| getRegexPattern | 0.003 | 0.001 | 0.003 | |
| getSeqsAcrossBSJs | 0.939 | 0.015 | 0.968 | |
| getSeqsFromGRs | 1.078 | 0.017 | 1.107 | |
| gtf | 0.033 | 0.002 | 0.036 | |
| gwasTraits | 0.008 | 0.002 | 0.011 | |
| importCircExplorer2 | 0.028 | 0.002 | 0.030 | |
| importCircMarker | 0.123 | 0.005 | 0.128 | |
| importKnife | 0.037 | 0.001 | 0.038 | |
| importMapSplice | 0.073 | 0.000 | 0.074 | |
| importNCLscan | 0.025 | 0.001 | 0.026 | |
| importOther | 0.022 | 0.001 | 0.023 | |
| importUroborus | 0.024 | 0.001 | 0.025 | |
| initCircRNAprofiler | 0.006 | 0.001 | 0.007 | |
| iupac | 0.003 | 0.003 | 0.005 | |
| liftBSJcoords | 0.653 | 0.009 | 0.667 | |
| mergeBSJunctions | 6.110 | 0.168 | 6.344 | |
| mergeMotifs | 20.638 | 0.076 | 21.663 | |
| mergedBSJunctions | 0.640 | 0.010 | 0.659 | |
| miRspeciesCodes | 0.003 | 0.002 | 0.006 | |
| plotExBetweenBSEs | 1.271 | 0.016 | 1.302 | |
| plotExPosition | 1.287 | 0.013 | 1.316 | |
| plotHostGenes | 1.165 | 0.012 | 1.183 | |
| plotLenBSEs | 2.864 | 0.062 | 2.955 | |
| plotLenIntrons | 1.848 | 0.048 | 1.914 | |
| plotMiR | 0.965 | 0.018 | 0.996 | |
| plotMotifs | 31.228 | 0.128 | 33.221 | |
| plotTotExons | 1.105 | 0.011 | 1.122 | |
| rearrangeMiRres | 0.842 | 0.015 | 0.866 | |
| volcanoPlot | 5.763 | 0.072 | 5.897 | |