Jianhong Ou
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/ribosomeProfilingQC |
| Branch: RELEASE_3_11 |
| Last Commit: a6e6817 |
| Last Changed Date: 2020-08-05 15:41:53 -0400 (Wed, 05 Aug 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:59:25 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE ribosomeProfilingQC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1490/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ribosomeProfilingQC 1.0.6 Jianhong Ou
| 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: ribosomeProfilingQC |
| Version: 1.0.6 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ribosomeProfilingQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ribosomeProfilingQC_1.0.6.tar.gz |
| StartedAt: 2020-10-17 04:37:53 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:49:04 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 671.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ribosomeProfilingQC.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ribosomeProfilingQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ribosomeProfilingQC_1.0.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ribosomeProfilingQC.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 ‘ribosomeProfilingQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ribosomeProfilingQC’ version ‘1.0.6’
* 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 ‘ribosomeProfilingQC’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
readsDistribution 12.081 0.271 12.359
coverageRates 11.324 0.184 11.514
coverageDepth 10.251 0.247 10.510
countReads 8.724 0.283 9.019
readsEndPlot 7.319 1.187 8.511
shiftReadsByFrame 7.965 0.122 8.091
strandPlot 5.672 0.052 5.734
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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
ribosomeProfilingQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ribosomeProfilingQC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘ribosomeProfilingQC’ ... ** using staged installation ** R ** 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 (ribosomeProfilingQC)
ribosomeProfilingQC.Rcheck/tests/runTests.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.
> require("ribosomeProfilingQC") || stop("unable to load Package:ribosomeProfilingQC")
Loading required package: ribosomeProfilingQC
Loading required package: GenomicRanges
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: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
[1] TRUE
> require("GenomicRanges") || stop("unable to load Package::GenomicRanges")
[1] TRUE
> require("GenomicFeatures") || stop("unable to load Package::GenomicFeatures")
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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")'.
[1] TRUE
> require("GenomicAlignments") || stop("unalbe to load Package:GenomicAlignments")
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
[1] TRUE
> require("utils") || stop("unable to load Package:utils")
[1] TRUE
> require("AnnotationDbi") || stop("unable to load Package:AnnotationDbi")
[1] TRUE
> require("BSgenome.Drerio.UCSC.danRer10") || stop("unable to load Package:BSgenome.Drerio.UCSC.danRer10")
Loading required package: BSgenome.Drerio.UCSC.danRer10
Loading required package: BSgenome
Loading required package: rtracklayer
[1] TRUE
> require("Rsamtools") || stop("unable to load Rsamtools")
[1] TRUE
> require("rtracklayer") || stop("unable to load rtracklayer")
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
[1] TRUE
> test_check("ribosomeProfilingQC")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 35 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 0 ]
>
> proc.time()
user system elapsed
112.317 2.382 117.563
ribosomeProfilingQC.Rcheck/ribosomeProfilingQC-Ex.timings
| name | user | system | elapsed | |
| FLOSS | 4.214 | 0.174 | 4.418 | |
| PAmotif | 0.152 | 0.011 | 0.162 | |
| assignReadingFrame | 1.771 | 0.091 | 1.864 | |
| codonUsage | 0.763 | 0.020 | 0.785 | |
| countReads | 8.724 | 0.283 | 9.019 | |
| coverageDepth | 10.251 | 0.247 | 10.510 | |
| coverageRates | 11.324 | 0.184 | 11.514 | |
| cvgd-class | 0.024 | 0.001 | 0.024 | |
| estimatePsite | 3.086 | 0.156 | 3.243 | |
| filterCDS | 0.280 | 0.013 | 0.293 | |
| frameCounts | 0.139 | 0.001 | 0.140 | |
| getFPKM | 0.032 | 0.002 | 0.034 | |
| getORFscore | 0.081 | 0.002 | 0.083 | |
| getPsiteCoordinates | 0.710 | 0.039 | 0.749 | |
| ggBar | 0.231 | 0.008 | 0.239 | |
| metaPlot | 0.001 | 0.001 | 0.000 | |
| normByRUVs | 0.000 | 0.000 | 0.001 | |
| plotDistance2Codon | 0.050 | 0.003 | 0.053 | |
| plotFrameDensity | 0.382 | 0.009 | 0.394 | |
| plotSpliceEvent | 0.000 | 0.000 | 0.001 | |
| plotTE | 0.076 | 0.005 | 0.082 | |
| plotTranscript | 0.129 | 0.007 | 0.137 | |
| prepareCDS | 0.745 | 0.016 | 0.812 | |
| readsDistribution | 12.081 | 0.271 | 12.359 | |
| readsEndPlot | 7.319 | 1.187 | 8.511 | |
| readsLenToKeep | 0.034 | 0.000 | 0.034 | |
| ribosomeReleaseScore | 0.000 | 0.001 | 0.001 | |
| shiftReadsByFrame | 7.965 | 0.122 | 8.091 | |
| simulateRPF | 2.681 | 0.039 | 2.723 | |
| spliceEvent | 0.001 | 0.000 | 0.001 | |
| strandPlot | 5.672 | 0.052 | 5.734 | |
| summaryReadsLength | 0.153 | 0.001 | 0.155 | |
| translationalEfficiency | 0 | 0 | 0 | |