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This page was generated on 2024-05-29 11:35:36 -0400 (Wed, 29 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4753
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4518
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

Package 1771/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ribosomeProfilingQC 1.16.0  (landing page)
Jianhong Ou
Snapshot Date: 2024-05-28 14:00:10 -0400 (Tue, 28 May 2024)
git_url: https://git.bioconductor.org/packages/ribosomeProfilingQC
git_branch: RELEASE_3_19
git_last_commit: 17cef85
git_last_commit_date: 2024-04-30 11:21:08 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for ribosomeProfilingQC on lconway


To the developers/maintainers of the ribosomeProfilingQC package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ribosomeProfilingQC
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ribosomeProfilingQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ribosomeProfilingQC_1.16.0.tar.gz
StartedAt: 2024-05-28 23:48:55 -0400 (Tue, 28 May 2024)
EndedAt: 2024-05-28 23:58:49 -0400 (Tue, 28 May 2024)
EllapsedTime: 593.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ribosomeProfilingQC.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ribosomeProfilingQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ribosomeProfilingQC_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ribosomeProfilingQC.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ribosomeProfilingQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ribosomeProfilingQC’ version ‘1.16.0’
* 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 code 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
codonBias         15.129  0.695  16.073
readsDistribution 14.821  0.488  15.476
coverageRates      8.412  0.272   8.778
readsEndPlot       6.502  1.404   8.037
coverageDepth      7.422  0.319   7.819
shiftReadsByFrame  5.973  0.248   6.294
countReads         5.668  0.119   5.846
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

ribosomeProfilingQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ribosomeProfilingQC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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)

Tests output

ribosomeProfilingQC.Rcheck/tests/runTests.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

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

    FileForFormat

[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 8 | SKIP 0 | PASS 35 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 35 ]
> 
> proc.time()
   user  system elapsed 
 89.874   3.474  94.340 

Example timings

ribosomeProfilingQC.Rcheck/ribosomeProfilingQC-Ex.timings

nameusersystemelapsed
FLOSS3.0310.2073.302
PAmotif0.1320.0100.143
assignReadingFrame2.4760.1102.614
codonBias15.129 0.69516.073
codonUsage0.3930.0260.424
countReads5.6680.1195.846
coverageDepth7.4220.3197.819
coverageRates8.4120.2728.778
cvgd-class0.0170.0010.019
estimatePsite2.9860.2433.261
filterCDS0.2480.0160.267
frameCounts0.0970.0020.098
getFPKM0.0070.0020.011
getORFscore0.0390.0020.041
getPsiteCoordinates0.6580.0420.705
ggBar0.2170.0370.260
metaPlot000
normBy1.2240.0821.315
normByRUVs000
normalizeTEbyLoess1.0920.0421.146
plotDistance2Codon0.0630.0030.066
plotFrameDensity0.2650.0120.281
plotSpliceEvent000
plotTE0.3940.0240.422
plotTranscript0.1160.0070.124
prepareCDS0.6420.0340.684
readsDistribution14.821 0.48815.476
readsEndPlot6.5021.4048.037
readsLenToKeep0.0360.0010.037
ribosomeReleaseScore000
shiftReadsByFrame5.9730.2486.294
simulateRPF1.9930.0462.058
spliceEvent0.0000.0000.001
strandPlot3.4840.1393.658
summaryReadsLength0.3760.0190.403
translationalEfficiency000