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This page was generated on 2024-03-28 11:32:29 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
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 1751/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ribosomeProfilingQC 1.14.1 (landing page) Jianhong Ou
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the ribosomeProfilingQC package: - 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. |
Package: ribosomeProfilingQC |
Version: 1.14.1 |
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_1.14.1.tar.gz |
StartedAt: 2024-03-28 00:32:55 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 00:42:13 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 558.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ribosomeProfilingQC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.14.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/ribosomeProfilingQC.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ribosomeProfilingQC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ribosomeProfilingQC’ version ‘1.14.1’ * 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 16.675 0.369 17.196 coverageRates 8.493 0.299 8.959 coverageDepth 7.658 0.244 7.968 countReads 7.210 0.200 7.464 shiftReadsByFrame 5.533 0.158 5.764 readsEndPlot 4.741 0.550 5.473 * 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/Resources/bin/R CMD INSTALL ribosomeProfilingQC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 (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 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 11 | SKIP 0 | PASS 35 ] [ FAIL 0 | WARN 11 | SKIP 0 | PASS 35 ] > > proc.time() user system elapsed 83.612 2.288 87.474
ribosomeProfilingQC.Rcheck/ribosomeProfilingQC-Ex.timings
name | user | system | elapsed | |
FLOSS | 3.452 | 0.147 | 3.656 | |
PAmotif | 0.136 | 0.010 | 0.147 | |
assignReadingFrame | 2.674 | 0.074 | 2.764 | |
codonUsage | 0.501 | 0.025 | 0.536 | |
countReads | 7.210 | 0.200 | 7.464 | |
coverageDepth | 7.658 | 0.244 | 7.968 | |
coverageRates | 8.493 | 0.299 | 8.959 | |
cvgd-class | 0.015 | 0.000 | 0.016 | |
estimatePsite | 3.348 | 0.173 | 3.548 | |
filterCDS | 0.226 | 0.012 | 0.239 | |
frameCounts | 0.089 | 0.001 | 0.090 | |
getFPKM | 0.013 | 0.002 | 0.015 | |
getORFscore | 0.057 | 0.007 | 0.065 | |
getPsiteCoordinates | 2.165 | 0.069 | 2.258 | |
ggBar | 0.221 | 0.009 | 0.236 | |
metaPlot | 0.001 | 0.000 | 0.000 | |
normByRUVs | 0 | 0 | 0 | |
plotDistance2Codon | 0.040 | 0.004 | 0.044 | |
plotFrameDensity | 0.219 | 0.013 | 0.238 | |
plotSpliceEvent | 0 | 0 | 0 | |
plotTE | 0.041 | 0.006 | 0.047 | |
plotTranscript | 0.082 | 0.002 | 0.085 | |
prepareCDS | 0.444 | 0.014 | 0.464 | |
readsDistribution | 16.675 | 0.369 | 17.196 | |
readsEndPlot | 4.741 | 0.550 | 5.473 | |
readsLenToKeep | 0.025 | 0.001 | 0.026 | |
ribosomeReleaseScore | 0 | 0 | 0 | |
shiftReadsByFrame | 5.533 | 0.158 | 5.764 | |
simulateRPF | 1.514 | 0.019 | 1.550 | |
spliceEvent | 0 | 0 | 0 | |
strandPlot | 3.843 | 0.132 | 4.043 | |
summaryReadsLength | 0.097 | 0.001 | 0.146 | |
translationalEfficiency | 0 | 0 | 0 | |