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This page was generated on 2024-04-18 11:32:17 -0400 (Thu, 18 Apr 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" | 4388 |
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 1773/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RNAmodR 1.16.0 (landing page) Felix G.M. Ernst
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the RNAmodR 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: RNAmodR |
Version: 1.16.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RNAmodR_1.16.0.tar.gz |
StartedAt: 2024-04-18 01:36:27 -0400 (Thu, 18 Apr 2024) |
EndedAt: 2024-04-18 01:50:30 -0400 (Thu, 18 Apr 2024) |
EllapsedTime: 842.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RNAmodR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RNAmodR_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/RNAmodR.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 ‘RNAmodR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RNAmodR’ 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 ‘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 56.029 5.110 56.102 CoverageSequenceData-class 16.209 1.323 20.960 ModInosine 10.401 0.366 12.642 EndSequenceData-class 8.281 0.391 10.503 ProtectedEndSequenceData-class 7.421 0.351 9.687 PileupSequenceData-class 6.749 0.357 9.174 * 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-3.18-bioc-mac-arm64/meat/RNAmodR.Rcheck/00check.log’ for details.
RNAmodR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RNAmodR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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 4.3.3 (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. > library(testthat) > library(RNAmodR) Loading required package: S4Vectors 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 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: 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") [E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/e2885269c6fa_2547' [E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/e2885269c6fa_2547' [E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/e2885269c6fa_2547' [E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/e2885269c6fa_2547' [E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/e2885269c6fa_2547' [E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/e2885269c6fa_2547' [ FAIL 0 | WARN 2 | SKIP 9 | PASS 192 ] ══ Skipped tests (9) ═══════════════════════════════════════════════════════════ • On Bioconductor (9): 'test-0SequenceData.R:53:3', 'test-0SequenceDataFrame.R:23:3', 'test-1SequenceDataSet.R:57:3', 'test-2Modifier.R:85:3', 'test-3normalization.R:3:3', 'test-3subset.R:4:3', 'test-3zcomparison.R:4:3', 'test-4roc.R:3:3', 'test-8visualization.R:158:3' [ FAIL 0 | WARN 2 | SKIP 9 | PASS 192 ] > > proc.time() user system elapsed 60.321 2.498 66.089
RNAmodR.Rcheck/RNAmodR-Ex.timings
name | user | system | elapsed | |
CoverageSequenceData-class | 16.209 | 1.323 | 20.960 | |
EndSequenceData-class | 8.281 | 0.391 | 10.503 | |
ModInosine-functions | 0.887 | 0.023 | 0.910 | |
ModInosine | 10.401 | 0.366 | 12.642 | |
Modifier-functions | 0.271 | 0.010 | 0.280 | |
NormEndSequenceData-class | 0 | 0 | 0 | |
PileupSequenceData-class | 6.749 | 0.357 | 9.174 | |
ProtectedEndSequenceData-class | 7.421 | 0.351 | 9.687 | |
RNAmodR-development | 0.069 | 0.002 | 0.071 | |
SequenceData-functions | 0.074 | 0.005 | 0.078 | |
SequenceDataFrame-class | 0.072 | 0.002 | 0.074 | |
SequenceDataList-class | 0.137 | 0.004 | 0.141 | |
SequenceDataSet-class | 0.108 | 0.008 | 0.116 | |
SequenceModDNAStringSetTrack-class | 1.981 | 0.014 | 1.995 | |
SequenceModRNAStringSetTrack-class | 0.119 | 0.002 | 0.121 | |
aggregate | 0.557 | 0.009 | 0.566 | |
compareByCoord | 2.098 | 0.039 | 2.147 | |
modify | 0.571 | 0.007 | 0.741 | |
plotData | 2.528 | 0.015 | 2.547 | |
plotROC | 1.373 | 0.019 | 1.394 | |
settings | 0.151 | 0.006 | 0.157 | |
stats | 56.029 | 5.110 | 56.102 | |
subsetByCoord | 0.605 | 0.005 | 0.610 | |