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This page was generated on 2022-12-06 11:06:33 -0500 (Tue, 06 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4277
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4193
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for ribosomeProfilingQC on nebbiolo1


To the developers/maintainers of the ribosomeProfilingQC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ribosomeProfilingQC.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1663/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ribosomeProfilingQC 1.11.0  (landing page)
Jianhong Ou
Snapshot Date: 2022-12-05 14:00:11 -0500 (Mon, 05 Dec 2022)
git_url: https://git.bioconductor.org/packages/ribosomeProfilingQC
git_branch: master
git_last_commit: 7a127d6
git_last_commit_date: 2022-11-01 11:21:25 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'BSgenome' which is not available

Summary

Package: ribosomeProfilingQC
Version: 1.11.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ribosomeProfilingQC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ribosomeProfilingQC_1.11.0.tar.gz
StartedAt: 2022-12-05 22:56:35 -0500 (Mon, 05 Dec 2022)
EndedAt: 2022-12-05 23:07:47 -0500 (Mon, 05 Dec 2022)
EllapsedTime: 672.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ribosomeProfilingQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ribosomeProfilingQC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ribosomeProfilingQC_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ribosomeProfilingQC.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘ribosomeProfilingQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ribosomeProfilingQC’ version ‘1.11.0’
* 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 ‘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 10.232  0.340  10.573
coverageRates      7.292  0.216   7.509
countReads         5.139  0.256   5.398
shiftReadsByFrame  5.321  0.072   5.394
coverageDepth      5.301  0.088   5.389
readsEndPlot       5.078  0.196   5.274
* 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 ...
  ‘ribosomeProfilingQC.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

ribosomeProfilingQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ribosomeProfilingQC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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)

Tests output

ribosomeProfilingQC.Rcheck/tests/runTests.Rout


R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences"
Copyright (C) 2022 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.

> require("ribosomeProfilingQC") || stop("unable to load Package:ribosomeProfilingQC")
Loading required package: ribosomeProfilingQC
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, aperm, 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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

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: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

The following object is masked from 'package:Biobase':

    rowMedians

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")
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 35 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 35 ]
> 
> proc.time()
   user  system elapsed 
 68.367   2.456  70.818 

Example timings

ribosomeProfilingQC.Rcheck/ribosomeProfilingQC-Ex.timings

nameusersystemelapsed
FLOSS2.9530.1283.115
PAmotif0.0930.0040.097
assignReadingFrame2.2220.0642.286
codonUsage0.4360.0120.449
countReads5.1390.2565.398
coverageDepth5.3010.0885.389
coverageRates7.2920.2167.509
cvgd-class0.0150.0000.015
estimatePsite2.5020.0482.550
filterCDS0.1640.0000.164
frameCounts0.0860.0000.086
getFPKM0.0080.0000.009
getORFscore0.0360.0000.036
getPsiteCoordinates0.5570.0040.561
ggBar0.1570.0000.157
metaPlot000
normByRUVs000
plotDistance2Codon0.0340.0040.037
plotFrameDensity0.2600.0280.289
plotSpliceEvent000
plotTE0.030.000.03
plotTranscript0.0660.0000.067
prepareCDS0.4130.0040.417
readsDistribution10.232 0.34010.573
readsEndPlot5.0780.1965.274
readsLenToKeep0.0220.0000.021
ribosomeReleaseScore0.0010.0000.000
shiftReadsByFrame5.3210.0725.394
simulateRPF1.6170.0161.633
spliceEvent0.0000.0000.001
strandPlot2.9280.0402.969
summaryReadsLength0.1220.0040.126
translationalEfficiency0.0010.0000.001