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 12:15:57 -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: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings circRNAprofiler_1.0.0.tar.gz |
| StartedAt: 2020-04-15 06:42:59 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:53:47 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 647.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: circRNAprofiler.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings circRNAprofiler_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/circRNAprofiler.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 25.300 0.068 28.154
getMotifs 16.732 0.116 18.904
mergeMotifs 15.460 0.056 16.883
getDeseqRes 6.124 0.148 6.412
getMiRsites 5.692 0.092 8.264
volcanoPlot 5.620 0.064 5.810
* 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: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL circRNAprofiler ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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-pc-linux-gnu (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
175.036 5.960 191.995
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
| name | user | system | elapsed | |
| ahChainFiles | 0.232 | 0.004 | 0.237 | |
| ahRepeatMasker | 0.000 | 0.000 | 0.003 | |
| annotateBSJs | 0.688 | 0.072 | 0.856 | |
| annotateRepeats | 1.552 | 0.080 | 1.700 | |
| annotateSNPsGWAS | 2.884 | 0.100 | 3.155 | |
| attractSpecies | 0.004 | 0.000 | 0.002 | |
| backSplicedJunctions | 0.772 | 0.016 | 0.801 | |
| checkProjectFolder | 0.004 | 0.000 | 0.003 | |
| filterCirc | 0.936 | 0.032 | 0.972 | |
| formatGTF | 0.000 | 0.000 | 0.001 | |
| getBackSplicedJunctions | 0.004 | 0.000 | 0.002 | |
| getCircSeqs | 0.904 | 0.064 | 0.972 | |
| getDeseqRes | 6.124 | 0.148 | 6.412 | |
| getDetectionTools | 0.004 | 0.000 | 0.003 | |
| getEdgerRes | 1.080 | 0.056 | 1.137 | |
| getMiRsites | 5.692 | 0.092 | 8.264 | |
| getMotifs | 16.732 | 0.116 | 18.904 | |
| getRandomBSJunctions | 0.080 | 0.016 | 0.098 | |
| getRegexPattern | 0.004 | 0.000 | 0.003 | |
| getSeqsAcrossBSJs | 0.912 | 0.092 | 1.008 | |
| getSeqsFromGRs | 0.956 | 0.064 | 1.022 | |
| gtf | 0.040 | 0.024 | 0.063 | |
| gwasTraits | 0.008 | 0.000 | 0.010 | |
| importCircExplorer2 | 0.024 | 0.000 | 0.051 | |
| importCircMarker | 0.128 | 0.016 | 0.230 | |
| importKnife | 0.028 | 0.004 | 0.091 | |
| importMapSplice | 0.068 | 0.000 | 0.068 | |
| importNCLscan | 0.020 | 0.000 | 0.023 | |
| importOther | 0.016 | 0.000 | 0.037 | |
| importUroborus | 0.020 | 0.004 | 0.028 | |
| initCircRNAprofiler | 0.008 | 0.000 | 0.006 | |
| iupac | 0.000 | 0.000 | 0.002 | |
| liftBSJcoords | 0.548 | 0.028 | 0.617 | |
| mergeBSJunctions | 4.084 | 0.024 | 4.162 | |
| mergeMotifs | 15.460 | 0.056 | 16.883 | |
| mergedBSJunctions | 0.584 | 0.036 | 0.620 | |
| miRspeciesCodes | 0.000 | 0.004 | 0.004 | |
| plotExBetweenBSEs | 1.172 | 0.052 | 1.226 | |
| plotExPosition | 1.076 | 0.056 | 1.134 | |
| plotHostGenes | 1.020 | 0.068 | 1.094 | |
| plotLenBSEs | 1.796 | 0.052 | 1.853 | |
| plotLenIntrons | 1.424 | 0.064 | 1.498 | |
| plotMiR | 0.856 | 0.072 | 0.933 | |
| plotMotifs | 25.300 | 0.068 | 28.154 | |
| plotTotExons | 1.120 | 0.064 | 1.191 | |
| rearrangeMiRres | 0.892 | 0.092 | 0.996 | |
| volcanoPlot | 5.620 | 0.064 | 5.810 | |