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This page was generated on 2024-05-18 11:37:16 -0400 (Sat, 18 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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: 2024-05-17 14:00:11 -0400 (Fri, 17 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
palomino3Windows Server 2022 Datacenter / x64  OK    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 palomino3


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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ribosomeProfilingQC.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ribosomeProfilingQC_1.16.0.tar.gz
StartedAt: 2024-05-18 05:50:49 -0400 (Sat, 18 May 2024)
EndedAt: 2024-05-18 06:00:51 -0400 (Sat, 18 May 2024)
EllapsedTime: 601.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ribosomeProfilingQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ribosomeProfilingQC.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ribosomeProfilingQC_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/ribosomeProfilingQC.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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
readsDistribution 14.24   0.52   14.78
codonBias         13.14   0.92   70.34
coverageRates      8.24   0.50    8.77
shiftReadsByFrame  7.67   0.18    7.89
readsEndPlot       6.64   0.27    6.96
coverageDepth      6.22   0.33    6.62
countReads         5.40   0.10    5.60
FLOSS              2.62   0.16   45.24
* 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:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL ribosomeProfilingQC
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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 version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

Attaching package: 'IRanges'

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

    windows

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 
  78.00    3.26   81.64 

Example timings

ribosomeProfilingQC.Rcheck/ribosomeProfilingQC-Ex.timings

nameusersystemelapsed
FLOSS 2.62 0.1645.24
PAmotif1.240.011.25
assignReadingFrame0.850.130.98
codonBias13.14 0.9270.34
codonUsage0.390.040.44
countReads5.40.15.6
coverageDepth6.220.336.62
coverageRates8.240.508.77
cvgd-class0.010.000.01
estimatePsite2.830.183.05
filterCDS0.230.040.27
frameCounts0.090.000.09
getFPKM0.020.000.01
getORFscore0.080.000.08
getPsiteCoordinates0.540.070.63
ggBar0.220.050.39
metaPlot000
normBy1.110.061.17
normByRUVs000
normalizeTEbyLoess1.030.001.05
plotDistance2Codon0.070.000.06
plotFrameDensity0.280.000.33
plotSpliceEvent000
plotTE0.480.000.50
plotTranscript0.140.000.14
prepareCDS0.530.000.55
readsDistribution14.24 0.5214.78
readsEndPlot6.640.276.96
readsLenToKeep0.030.000.03
ribosomeReleaseScore000
shiftReadsByFrame7.670.187.89
simulateRPF1.520.031.54
spliceEvent000
strandPlot3.560.183.74
summaryReadsLength0.160.000.15
translationalEfficiency000