Bora Uyar
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/RCAS |
| Branch: RELEASE_3_9 |
| Last Commit: 909750b |
| Last Changed Date: 2019-07-10 10:22:11 -0400 (Wed, 10 Jul 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:58:23 -0400 (Wed, 16 Oct 2019).
| Package 1323/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RCAS 1.10.1 Bora Uyar
| 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 | |
| Package: RCAS |
| Version: 1.10.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RCAS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RCAS_1.10.1.tar.gz |
| StartedAt: 2019-10-16 06:01:59 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:19:23 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 1044.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RCAS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RCAS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RCAS_1.10.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/RCAS.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCAS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCAS’ version ‘1.10.1’
* 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 ‘RCAS’ 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 ... NOTE
Namespace in Imports field not imported from: ‘DBI’
All declared Imports should be used.
* 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
runMotifRG 55.103 19.372 43.914
getMotifSummaryTable 53.987 19.339 42.835
getFeatureBoundaryCoverageMulti 24.514 3.250 27.965
calculateCoverageProfileList 19.109 2.502 21.630
calculateCoverageProfile 18.846 1.572 20.427
calculateCoverageProfileListFromTxdb 17.084 2.191 19.281
summarizeQueryRegionsMulti 15.299 1.824 40.347
getTargetedGenesTable 14.974 1.794 16.530
getTxdbFeaturesFromGRanges 13.930 1.490 17.369
getTxdbFeatures 13.838 1.385 15.438
summarizeQueryRegions 12.984 1.374 14.615
calculateCoverageProfileFromTxdb 9.979 1.011 10.994
plotFeatureBoundaryCoverage 9.115 1.387 10.433
getFeatureBoundaryCoverageBin 9.406 1.038 10.451
getFeatureBoundaryCoverage 7.833 0.842 8.678
createDB 4.639 0.174 26.957
retrieveOrthologs 0.721 0.043 9.857
createOrthologousGeneSetList 0.658 0.055 27.908
* 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/RCAS.Rcheck/00check.log’
for details.
RCAS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RCAS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘RCAS’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package can be loaded from final location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package keeps a record of temporary installation path * DONE (RCAS)
RCAS.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(RCAS)
Loading required package: plotly
Loading required package: ggplot2
Attaching package: 'plotly'
The following object is masked from 'package:ggplot2':
last_plot
The following object is masked from 'package:stats':
filter
The following object is masked from 'package:graphics':
layout
Loading required package: DT
Loading required package: data.table
Loading required package: topGO
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: graph
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: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:data.table':
first, second
The following object is masked from 'package:plotly':
rename
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:data.table':
shift
The following object is masked from 'package:plotly':
slice
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:plotly':
select
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: 'topGO'
The following object is masked from 'package:IRanges':
members
Loading required package: motifRG
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:graph':
complement
The following object is masked from 'package:base':
strsplit
Loading required package: seqLogo
Loading required package: grid
Attaching package: 'grid'
The following object is masked from 'package:topGO':
depth
Loading required package: BSgenome
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: rtracklayer
Attaching package: 'rtracklayer'
The following object is masked from 'package:plotly':
export
Loading required package: BSgenome.Hsapiens.UCSC.hg19
>
> test_check("RCAS")
GAAGGA 1.475e-06
Skip pattern ATTTTT
Refine GAAGGA 11.39794 : 11.74262 11.42128 12.13374 10.58774 11.37687 TRUE 463 156 449 147
New motif: GAAGGA
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 81 | SKIPPED: 0 | WARNINGS: 71 | FAILED: 0 ]
>
> proc.time()
user system elapsed
144.345 26.220 165.856
RCAS.Rcheck/RCAS-Ex.timings
| name | user | system | elapsed | |
| calculateCoverageProfile | 18.846 | 1.572 | 20.427 | |
| calculateCoverageProfileFromTxdb | 9.979 | 1.011 | 10.994 | |
| calculateCoverageProfileList | 19.109 | 2.502 | 21.630 | |
| calculateCoverageProfileListFromTxdb | 17.084 | 2.191 | 19.281 | |
| createControlRegions | 0.484 | 0.007 | 0.491 | |
| createDB | 4.639 | 0.174 | 26.957 | |
| createOrthologousGeneSetList | 0.658 | 0.055 | 27.908 | |
| discoverFeatureSpecificMotifs | 0 | 0 | 0 | |
| extractSequences | 2.065 | 0.301 | 2.367 | |
| getFeatureBoundaryCoverage | 7.833 | 0.842 | 8.678 | |
| getFeatureBoundaryCoverageBin | 9.406 | 1.038 | 10.451 | |
| getFeatureBoundaryCoverageMulti | 24.514 | 3.250 | 27.965 | |
| getIntervalOverlapMatrix | 1.535 | 0.166 | 2.328 | |
| getMotifSummaryTable | 53.987 | 19.339 | 42.835 | |
| getTargetedGenesTable | 14.974 | 1.794 | 16.530 | |
| getTxdbFeatures | 13.838 | 1.385 | 15.438 | |
| getTxdbFeaturesFromGRanges | 13.930 | 1.490 | 17.369 | |
| importBed | 0.484 | 0.023 | 0.531 | |
| importBedFiles | 1.948 | 0.110 | 2.190 | |
| importGtf | 0.001 | 0.000 | 0.001 | |
| parseMsigdb | 0.004 | 0.001 | 0.005 | |
| plotFeatureBoundaryCoverage | 9.115 | 1.387 | 10.433 | |
| printMsigdbDataset | 0.339 | 0.288 | 0.116 | |
| queryGff | 0.816 | 0.190 | 0.951 | |
| retrieveOrthologs | 0.721 | 0.043 | 9.857 | |
| runGSEA | 1.655 | 0.227 | 1.890 | |
| runMotifRG | 55.103 | 19.372 | 43.914 | |
| runReport | 0.001 | 0.001 | 0.002 | |
| runReportMetaAnalysis | 1.852 | 0.406 | 2.385 | |
| runTopGO | 0.001 | 0.001 | 0.001 | |
| summarizeQueryRegions | 12.984 | 1.374 | 14.615 | |
| summarizeQueryRegionsMulti | 15.299 | 1.824 | 40.347 | |