Bora Uyar
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/RCAS |
| Branch: RELEASE_3_7 |
| Last Commit: c347094 |
| Last Changed Date: 2018-04-30 10:35:43 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:56:52 -0400 (Wed, 17 Oct 2018).
| Package 1193/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RCAS 1.6.0 Bora Uyar
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: RCAS |
| Version: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2018-10-16 23:32:53 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 23:47:42 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 888.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RCAS.Rcheck |
| Warnings: 0 |
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###
### 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_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/RCAS.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.6.0’
* 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 49.939 11.235 38.801
getMotifSummaryTable 47.883 11.142 34.757
getFeatureBoundaryCoverageMulti 30.102 1.572 32.267
calculateCoverageProfileList 23.310 1.226 24.823
calculateCoverageProfile 21.395 0.918 22.549
calculateCoverageProfileListFromTxdb 20.767 1.095 22.104
summarizeQueryRegionsMulti 20.862 0.843 37.967
getTxdbFeatures 18.815 0.708 19.663
summarizeQueryRegions 18.107 0.705 19.050
getTargetedGenesTable 17.131 0.729 18.032
calculateCoverageProfileFromTxdb 14.311 0.580 15.064
getTxdbFeaturesFromGRanges 13.754 0.596 14.411
getFeatureBoundaryCoverage 13.673 0.576 14.553
plotFeatureBoundaryCoverage 13.754 0.460 14.349
getFeatureBoundaryCoverageBin 13.225 0.454 13.926
createDB 4.005 0.059 20.250
createOrthologousGeneSetList 0.486 0.032 14.740
retrieveOrthologs 0.324 0.050 11.199
* 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-3.7-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/3.5/Resources/library’ * installing *source* package ‘RCAS’ ... ** 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 groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. * DONE (RCAS)
RCAS.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, 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")
GAAGAA 1.554582e-06
Refine GAAGAA 11.75173 : 12.09648 11.52659 11.44651 12.5975 12.79872 TRUE 623 231 566 212
New motif: GAAGAA
══ testthat results ═══════════════════════════════════════════════════════════
OK: 102 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
126.162 13.445 140.975
RCAS.Rcheck/RCAS-Ex.timings
| name | user | system | elapsed | |
| calculateCoverageProfile | 21.395 | 0.918 | 22.549 | |
| calculateCoverageProfileFromTxdb | 14.311 | 0.580 | 15.064 | |
| calculateCoverageProfileList | 23.310 | 1.226 | 24.823 | |
| calculateCoverageProfileListFromTxdb | 20.767 | 1.095 | 22.104 | |
| createControlRegions | 0.408 | 0.005 | 0.426 | |
| createDB | 4.005 | 0.059 | 20.250 | |
| createOrthologousGeneSetList | 0.486 | 0.032 | 14.740 | |
| discoverFeatureSpecificMotifs | 0.002 | 0.000 | 0.002 | |
| extractSequences | 1.503 | 0.092 | 1.670 | |
| getFeatureBoundaryCoverage | 13.673 | 0.576 | 14.553 | |
| getFeatureBoundaryCoverageBin | 13.225 | 0.454 | 13.926 | |
| getFeatureBoundaryCoverageMulti | 30.102 | 1.572 | 32.267 | |
| getIntervalOverlapMatrix | 1.359 | 0.110 | 1.856 | |
| getMotifSummaryTable | 47.883 | 11.142 | 34.757 | |
| getTargetedGenesTable | 17.131 | 0.729 | 18.032 | |
| getTxdbFeatures | 18.815 | 0.708 | 19.663 | |
| getTxdbFeaturesFromGRanges | 13.754 | 0.596 | 14.411 | |
| importBed | 0.294 | 0.010 | 0.309 | |
| importBedFiles | 1.166 | 0.050 | 1.225 | |
| importGtf | 0.002 | 0.000 | 0.003 | |
| parseMsigdb | 0.004 | 0.000 | 0.004 | |
| plotFeatureBoundaryCoverage | 13.754 | 0.460 | 14.349 | |
| printMsigdbDataset | 0.062 | 0.004 | 0.066 | |
| queryGff | 0.663 | 0.082 | 0.755 | |
| retrieveOrthologs | 0.324 | 0.050 | 11.199 | |
| runGSEA | 1.501 | 0.084 | 1.610 | |
| runMotifRG | 49.939 | 11.235 | 38.801 | |
| runReport | 0.003 | 0.000 | 0.004 | |
| runReportMetaAnalysis | 1.499 | 0.195 | 1.770 | |
| runTopGO | 0.002 | 0.000 | 0.002 | |
| summarizeQueryRegions | 18.107 | 0.705 | 19.050 | |
| summarizeQueryRegionsMulti | 20.862 | 0.843 | 37.967 | |