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This page was generated on 2020-10-17 11:59:26 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE RNAmodR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1508/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
RNAmodR 1.2.3 Felix G.M. Ernst
| 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: RNAmodR |
Version: 1.2.3 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RNAmodR_1.2.3.tar.gz |
StartedAt: 2020-10-17 04:42:42 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 04:56:58 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 856.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RNAmodR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RNAmodR_1.2.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/RNAmodR.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 ‘RNAmodR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RNAmodR’ version ‘1.2.3’ * 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 ‘RNAmodR’ 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 ... NOTE Unexported objects imported by ':::' calls: 'BiocGenerics:::replaceSlots' 'Biostrings:::XString' 'IRanges:::.valid.CompressedList' 'IRanges:::coerceToCompressedList' 'S4Vectors:::.valid.DataFrame' 'S4Vectors:::labeledLine' 'S4Vectors:::make_zero_col_DataFrame' 'S4Vectors:::prepare_objects_to_bind' See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: '.get_inosine_score' * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed stats 89.339 9.668 73.670 CoverageSequenceData-class 22.942 1.359 25.688 ModInosine 16.877 0.231 17.974 EndSequenceData-class 15.425 0.293 16.390 ProtectedEndSequenceData-class 14.069 0.234 14.898 PileupSequenceData-class 13.482 0.219 14.336 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 1 NOTE See ‘/Users/biocbuild/bbs-3.11-bioc/meat/RNAmodR.Rcheck/00check.log’ for details.
RNAmodR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RNAmodR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘RNAmodR’ ... ** using staged installation ** R ** data ** 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 (RNAmodR)
RNAmodR.Rcheck/tests/testthat.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. > library(testthat) > library(RNAmodR) Loading required package: IRanges 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 Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: Modstrings Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'RNAmodR' The following object is masked from 'package:testthat': compare > > test_check("RNAmodR") ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 187 | SKIPPED: 9 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 76.853 2.239 82.896
RNAmodR.Rcheck/RNAmodR-Ex.timings
name | user | system | elapsed | |
CoverageSequenceData-class | 22.942 | 1.359 | 25.688 | |
EndSequenceData-class | 15.425 | 0.293 | 16.390 | |
ModInosine-functions | 1.069 | 0.016 | 1.192 | |
ModInosine | 16.877 | 0.231 | 17.974 | |
Modifier-functions | 0.356 | 0.010 | 0.366 | |
NormEndSequenceData-class | 0.000 | 0.001 | 0.001 | |
PileupSequenceData-class | 13.482 | 0.219 | 14.336 | |
ProtectedEndSequenceData-class | 14.069 | 0.234 | 14.898 | |
RNAmodR-development | 0.078 | 0.002 | 0.080 | |
SequenceData-functions | 0.104 | 0.007 | 0.113 | |
SequenceDataFrame-class | 0.113 | 0.003 | 0.117 | |
SequenceDataList-class | 0.203 | 0.007 | 0.211 | |
SequenceDataSet-class | 0.108 | 0.004 | 0.112 | |
SequenceModDNAStringSetTrack-class | 1.488 | 0.036 | 1.526 | |
SequenceModRNAStringSetTrack-class | 0.217 | 0.003 | 0.222 | |
aggregate | 0.879 | 0.012 | 0.896 | |
compareByCoord | 3.077 | 0.032 | 3.113 | |
modify | 0.871 | 0.006 | 0.878 | |
plotData | 2.522 | 0.013 | 2.541 | |
plotROC | 2.479 | 0.016 | 2.499 | |
settings | 0.171 | 0.004 | 0.174 | |
stats | 89.339 | 9.668 | 73.670 | |
subsetByCoord | 1.041 | 0.012 | 1.054 | |